|
CNC64A_044G00080 |
Notice (8): Undefined index: common_name [APP/View/Analysis/custom_tree_creation.ctp, line 169]Code Context echo "<td><input type='checkbox' name='selected_genes[]' value='".$similarity_hit['gene_id']."' ".$checked." /></td>\n";
echo "<td>".$this->Html->link($similarity_hit_gene,array("controller"=>"genes","action"=>"view",$similarity_hit_gene),array("target"=>"_blank"))."</td>\n";
echo "<td>".$this->Html->link($similarity_hit['common_name'],array("controller"=>"organism","action"=>"view",urlencode($similarity_hit['common_name'])))."</td>\n";
$viewFile = '/xtras/group/biocomp/plaza/versions/plaza_pico_03/app/View/Analysis/custom_tree_creation.ctp'
$dataForView = array(
'allowed_extra_sequences_types' => array(
'aa' => 'Protein',
'dna' => 'DNA'
),
'allowed_editing_methods' => array(
'column' => 'Positions only',
'row' => 'Genes only',
'column_row' => 'Positions and Genes',
'none' => 'No editing'
),
'allowed_tree_programs' => array(
'fasttree' => 'FastTree',
'iqtree' => 'IQ-TREE (includes model testing)',
'raxml' => 'RAxML',
'phyml' => 'PhyML'
),
'allowed_msa_programs' => array(
'muscle' => 'MUSCLE',
'mafft' => 'MAFFT'
),
'allowed_number_blasthits' => array(
(int) 0 => 'all',
(int) 1 => (int) 20,
(int) 2 => (int) 10,
(int) 3 => (int) 5,
(int) 4 => (int) 1
),
'similarity_hits_genes' => array(
'ENSMUSG00000093862' => array(
'gene_id' => 'ENSMUSG00000093862',
'e_value' => '0.0',
'bit_score' => '1786',
'alignment_length' => '858',
'identity_percentage' => '100.00',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
[maximum depth reached]
)
),
'ENSMUSG00000028233' => array(
'gene_id' => 'ENSMUSG00000028233',
'e_value' => '0.0',
'bit_score' => '1588',
'alignment_length' => '861',
'identity_percentage' => '91.41',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
[maximum depth reached]
)
),
'PP00092G00090' => array(
'gene_id' => 'PP00092G00090',
'e_value' => '9e-77',
'bit_score' => '270',
'alignment_length' => '205',
'identity_percentage' => '60.98',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'AT1G45231' => array(
'gene_id' => 'AT1G45231',
'e_value' => '2e-72',
'bit_score' => '253',
'alignment_length' => '297',
'identity_percentage' => '47.81',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'emh729020' => array(
'gene_id' => 'emh729020',
'e_value' => '2e-69',
'bit_score' => '239',
'alignment_length' => '205',
'identity_percentage' => '58.05',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'FBgn0266195' => array(
'gene_id' => 'FBgn0266195',
'e_value' => '5e-69',
'bit_score' => '242',
'alignment_length' => '233',
'identity_percentage' => '49.79',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
[maximum depth reached]
)
),
'AT1G30550' => array(
'gene_id' => 'AT1G30550',
'e_value' => '1e-68',
'bit_score' => '241',
'alignment_length' => '203',
'identity_percentage' => '55.67',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00019G00550' => array(
'gene_id' => 'ATR_00019G00550',
'e_value' => '1e-68',
'bit_score' => '236',
'alignment_length' => '223',
'identity_percentage' => '52.91',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'OS03G27930' => array(
'gene_id' => 'OS03G27930',
'e_value' => '5e-68',
'bit_score' => '245',
'alignment_length' => '204',
'identity_percentage' => '56.86',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'ES0120G00110' => array(
'gene_id' => 'ES0120G00110',
'e_value' => '4e-67',
'bit_score' => '239',
'alignment_length' => '226',
'identity_percentage' => '51.77',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00003G02210' => array(
'gene_id' => 'ATR_00003G02210',
'e_value' => '4e-66',
'bit_score' => '240',
'alignment_length' => '202',
'identity_percentage' => '56.44',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'WBGene00011631' => array(
'gene_id' => 'WBGene00011631',
'e_value' => '2e-65',
'bit_score' => '234',
'alignment_length' => '227',
'identity_percentage' => '55.95',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
[maximum depth reached]
)
),
'DDB_G0288547' => array(
'gene_id' => 'DDB_G0288547',
'e_value' => '9e-63',
'bit_score' => '220',
'alignment_length' => '212',
'identity_percentage' => '51.89',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
[maximum depth reached]
)
),
'Naga_100003g58' => array(
'gene_id' => 'Naga_100003g58',
'e_value' => '1e-61',
'bit_score' => '221',
'alignment_length' => '203',
'identity_percentage' => '54.19',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
[maximum depth reached]
)
),
'AC00G95840' => array(
'gene_id' => 'AC00G95840',
'e_value' => '7e-60',
'bit_score' => '207',
'alignment_length' => '206',
'identity_percentage' => '50.00',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
[maximum depth reached]
)
),
'phs121750' => array(
'gene_id' => 'phs121750',
'e_value' => '2e-58',
'bit_score' => '209',
'alignment_length' => '206',
'identity_percentage' => '50.00',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
[maximum depth reached]
)
),
'OS06G08800' => array(
'gene_id' => 'OS06G08800',
'e_value' => '2e-57',
'bit_score' => '204',
'alignment_length' => '206',
'identity_percentage' => '49.51',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'ccr132780' => array(
'gene_id' => 'ccr132780',
'e_value' => '2e-56',
'bit_score' => '199',
'alignment_length' => '213',
'identity_percentage' => '48.36',
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_044G00080' => array(
'gene_id' => 'CNC64A_044G00080',
'e_value' => '1e-53',
'bit_score' => '196',
'alignment_length' => '214',
'identity_percentage' => '47.20',
'gf' => array(
[maximum depth reached]
)
),
'OM_04G01940' => array(
'gene_id' => 'OM_04G01940',
'e_value' => '3e-53',
'bit_score' => '191',
'alignment_length' => '219',
'identity_percentage' => '44.29',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
[maximum depth reached]
)
),
'CV00G61210' => array(
'gene_id' => 'CV00G61210',
'e_value' => '8e-50',
'bit_score' => '179',
'alignment_length' => '211',
'identity_percentage' => '44.08',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.19g00730' => array(
'gene_id' => 'RCC4223.19g00730',
'e_value' => '7e-49',
'bit_score' => '185',
'alignment_length' => '261',
'identity_percentage' => '41.38',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G01490' => array(
'gene_id' => 'PI00G01490',
'e_value' => '2e-48',
'bit_score' => '184',
'alignment_length' => '306',
'identity_percentage' => '37.91',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'gsu74830' => array(
'gene_id' => 'gsu74830',
'e_value' => '9e-48',
'bit_score' => '175',
'alignment_length' => '230',
'identity_percentage' => '42.61',
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'gf' => array(
[maximum depth reached]
)
),
'CR06G11280' => array(
'gene_id' => 'CR06G11280',
'e_value' => '1e-46',
'bit_score' => '184',
'alignment_length' => '234',
'identity_percentage' => '42.74',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'AP00G00630' => array(
'gene_id' => 'AP00G00630',
'e_value' => '1e-44',
'bit_score' => '175',
'alignment_length' => '242',
'identity_percentage' => '41.74',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'TP02G08210' => array(
'gene_id' => 'TP02G08210',
'e_value' => '3e-42',
'bit_score' => '160',
'alignment_length' => '247',
'identity_percentage' => '38.46',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
[maximum depth reached]
)
),
'BPRRCC1105_14G03340' => array(
'gene_id' => 'BPRRCC1105_14G03340',
'e_value' => '1e-41',
'bit_score' => '156',
'alignment_length' => '183',
'identity_percentage' => '43.17',
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'gf' => array(
[maximum depth reached]
)
),
'SPAC2G11.15c' => array(
'gene_id' => 'SPAC2G11.15c',
'e_value' => '2e-41',
'bit_score' => '157',
'alignment_length' => '230',
'identity_percentage' => '39.13',
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'gf' => array(
[maximum depth reached]
)
),
'MRCC299_01G06910' => array(
'gene_id' => 'MRCC299_01G06910',
'e_value' => '1e-40',
'bit_score' => '160',
'alignment_length' => '247',
'identity_percentage' => '38.46',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
[maximum depth reached]
)
),
'OT_02G01350' => array(
'gene_id' => 'OT_02G01350',
'e_value' => '7e-39',
'bit_score' => '149',
'alignment_length' => '214',
'identity_percentage' => '38.79',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
[maximum depth reached]
)
),
'MP02G06160' => array(
'gene_id' => 'MP02G06160',
'e_value' => '1e-37',
'bit_score' => '149',
'alignment_length' => '254',
'identity_percentage' => '35.43',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
[maximum depth reached]
)
),
'PTI_22G00250' => array(
'gene_id' => 'PTI_22G00250',
'e_value' => '4e-34',
'bit_score' => '141',
'alignment_length' => '308',
'identity_percentage' => '32.79',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'CM19G03870' => array(
'gene_id' => 'CM19G03870',
'e_value' => '1e-33',
'bit_score' => '136',
'alignment_length' => '213',
'identity_percentage' => '38.03',
'species' => 'cme',
'common_name' => 'Cyanidioschyzon merolae',
'gf' => array(
[maximum depth reached]
)
),
'FC009G01340' => array(
'gene_id' => 'FC009G01340',
'e_value' => '5e-33',
'bit_score' => '134',
'alignment_length' => '229',
'identity_percentage' => '39.30',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
[maximum depth reached]
)
),
'AA0018G01160' => array(
'gene_id' => 'AA0018G01160',
'e_value' => '1e-31',
'bit_score' => '124',
'alignment_length' => '102',
'identity_percentage' => '54.90',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'YPL157W' => array(
'gene_id' => 'YPL157W',
'e_value' => '7e-29',
'bit_score' => '123',
'alignment_length' => '181',
'identity_percentage' => '38.67',
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'gf' => array(
[maximum depth reached]
)
),
'pte317770' => array(
'gene_id' => 'pte317770',
'e_value' => '1e-28',
'bit_score' => '121',
'alignment_length' => '216',
'identity_percentage' => '32.41',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'PTI_22G00920' => array(
'gene_id' => 'PTI_22G00920',
'e_value' => '3e-27',
'bit_score' => '119',
'alignment_length' => '172',
'identity_percentage' => '41.28',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'pte644480' => array(
'gene_id' => 'pte644480',
'e_value' => '1e-25',
'bit_score' => '112',
'alignment_length' => '231',
'identity_percentage' => '32.03',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'pte492450' => array(
'gene_id' => 'pte492450',
'e_value' => '3e-24',
'bit_score' => '108',
'alignment_length' => '231',
'identity_percentage' => '30.74',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'TP07G02910' => array(
'gene_id' => 'TP07G02910',
'e_value' => '8e-22',
'bit_score' => '97.8',
'alignment_length' => '125',
'identity_percentage' => '44.00',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
[maximum depth reached]
)
),
'OL02G04740' => array(
'gene_id' => 'OL02G04740',
'e_value' => '1e-18',
'bit_score' => '87.8',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
[maximum depth reached]
)
),
'FC004G05310' => array(
'gene_id' => 'FC004G05310',
'e_value' => '2e-18',
'bit_score' => '91.3',
'alignment_length' => '180',
'identity_percentage' => '35.00',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
[maximum depth reached]
)
),
'ORCC809_02G02560' => array(
'gene_id' => 'ORCC809_02G02560',
'e_value' => '4e-17',
'bit_score' => '82.8',
'alignment_length' => '79',
'identity_percentage' => '50.63',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
[maximum depth reached]
)
),
'pte690930' => array(
'gene_id' => 'pte690930',
'e_value' => '3e-15',
'bit_score' => '83.2',
'alignment_length' => '196',
'identity_percentage' => '30.61',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'pte615620' => array(
'gene_id' => 'pte615620',
'e_value' => '7e-14',
'bit_score' => '79.0',
'alignment_length' => '201',
'identity_percentage' => '29.85',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'Naga_100031g18' => array(
'gene_id' => 'Naga_100031g18',
'e_value' => '7e-14',
'bit_score' => '77.8',
'alignment_length' => '160',
'identity_percentage' => '29.38',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
[maximum depth reached]
)
),
'phs302960' => array(
'gene_id' => 'phs302960',
'e_value' => '5e-10',
'bit_score' => '67.0',
'alignment_length' => '138',
'identity_percentage' => '32.61',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
[maximum depth reached]
)
),
'ccr191460' => array(
'gene_id' => 'ccr191460',
'e_value' => '3e-07',
'bit_score' => '57.0',
'alignment_length' => '116',
'identity_percentage' => '33.62',
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'gf' => array(
[maximum depth reached]
)
),
'ES0387G00030' => array(
'gene_id' => 'ES0387G00030',
'e_value' => '1e-06',
'bit_score' => '53.1',
'alignment_length' => '124',
'identity_percentage' => '30.65',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
)
),
'similarity_hits_species' => array(
'mus' => array(
(int) 0 => 'ENSMUSG00000093862',
(int) 1 => 'ENSMUSG00000028233'
),
'ppa' => array(
(int) 0 => 'PP00092G00090'
),
'ath' => array(
(int) 0 => 'AT1G45231',
(int) 1 => 'AT1G30550'
),
'emh' => array(
(int) 0 => 'emh729020'
),
'drm' => array(
(int) 0 => 'FBgn0266195'
),
'atr' => array(
(int) 0 => 'ATR_00019G00550',
(int) 1 => 'ATR_00003G02210'
),
'osa' => array(
(int) 0 => 'OS03G27930',
(int) 1 => 'OS06G08800'
),
'esi' => array(
(int) 0 => 'ES0120G00110',
(int) 1 => 'ES0387G00030'
),
'cel' => array(
(int) 0 => 'WBGene00011631'
),
'ddi' => array(
(int) 0 => 'DDB_G0288547'
),
'nga' => array(
(int) 0 => 'Naga_100003g58',
(int) 1 => 'Naga_100031g18'
),
'acg' => array(
(int) 0 => 'AC00G95840'
),
'phs' => array(
(int) 0 => 'phs121750',
(int) 1 => 'phs302960'
),
'ccr' => array(
(int) 0 => 'ccr132780',
(int) 1 => 'ccr191460'
),
'ome' => array(
(int) 0 => 'OM_04G01940'
),
'cvu' => array(
(int) 0 => 'CV00G61210'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.19g00730'
),
'pse3' => array(
(int) 0 => 'PI00G01490'
),
'gsu' => array(
(int) 0 => 'gsu74830'
),
'cre' => array(
(int) 0 => 'CR06G11280'
),
'apr' => array(
(int) 0 => 'AP00G00630'
),
'tps' => array(
(int) 0 => 'TP02G08210',
(int) 1 => 'TP07G02910'
),
'bprrcc1105' => array(
(int) 0 => 'BPRRCC1105_14G03340'
),
'scp' => array(
(int) 0 => 'SPAC2G11.15c'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_01G06910'
),
'ota' => array(
(int) 0 => 'OT_02G01350'
),
'mpu' => array(
(int) 0 => 'MP02G06160'
),
'ptri' => array(
(int) 0 => 'PTI_22G00250',
(int) 1 => 'PTI_22G00920'
),
'cme' => array(
(int) 0 => 'CM19G03870'
),
'fcy' => array(
(int) 0 => 'FC009G01340',
(int) 1 => 'FC004G05310'
),
'aan' => array(
(int) 0 => 'AA0018G01160'
),
'sac' => array(
(int) 0 => 'YPL157W'
),
'pte' => array(
(int) 0 => 'pte317770',
(int) 1 => 'pte644480',
(int) 2 => 'pte492450',
(int) 3 => 'pte690930',
(int) 4 => 'pte615620'
),
'olu' => array(
(int) 0 => 'OL02G04740'
),
'orcc809' => array(
(int) 0 => 'ORCC809_02G02560'
)
),
'gene_id' => 'ENSMUSG00000093862',
'all_species_index' => array(
(int) 0 => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333'
),
(int) 1 => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702'
),
(int) 2 => array(
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'tax_id' => '763042'
),
(int) 3 => array(
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'tax_id' => '44056'
),
(int) 4 => array(
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'tax_id' => '3075'
),
(int) 5 => array(
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'tax_id' => '41875'
),
(int) 6 => array(
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'tax_id' => '6239'
),
(int) 7 => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055'
),
(int) 8 => array(
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'tax_id' => '310507'
),
(int) 9 => array(
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'tax_id' => '2769'
),
(int) 10 => array(
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'tax_id' => '574566'
),
(int) 11 => array(
'species' => 'cme',
'common_name' => 'Cyanidioschyzon merolae',
'tax_id' => '45157'
),
(int) 12 => array(
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'tax_id' => '44689'
),
(int) 13 => array(
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'tax_id' => '7227'
),
(int) 14 => array(
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'tax_id' => '2880'
),
(int) 15 => array(
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'tax_id' => '280463'
),
(int) 16 => array(
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'tax_id' => '186039'
),
(int) 17 => array(
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'tax_id' => '130081'
),
(int) 18 => array(
'species' => 'hsp',
'common_name' => 'Helicosporidium sp. ',
'tax_id' => '145475'
),
(int) 19 => array(
'species' => 'hom',
'common_name' => 'Homo sapiens',
'tax_id' => '9606'
),
(int) 20 => array(
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'tax_id' => '564608'
),
(int) 21 => array(
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'tax_id' => '296587'
),
(int) 22 => array(
'species' => 'mus',
'common_name' => 'Mus musculus',
'tax_id' => '10090'
),
(int) 23 => array(
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'tax_id' => '72520'
),
(int) 24 => array(
'species' => 'osa',
'common_name' => 'Oryza sativa',
'tax_id' => '4530'
),
(int) 25 => array(
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'tax_id' => '242159'
),
(int) 26 => array(
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'tax_id' => '1486918'
),
(int) 27 => array(
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'tax_id' => '385169'
),
(int) 28 => array(
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'tax_id' => '70448'
),
(int) 29 => array(
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'tax_id' => '5888'
),
(int) 30 => array(
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'tax_id' => '2850'
),
(int) 31 => array(
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'tax_id' => '3218'
),
(int) 32 => array(
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'tax_id' => '67593'
),
(int) 33 => array(
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'tax_id' => '1470871'
),
(int) 34 => array(
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'tax_id' => '249344'
),
(int) 35 => array(
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'tax_id' => '4932'
),
(int) 36 => array(
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'tax_id' => '4896'
),
(int) 37 => array(
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'tax_id' => '35128'
),
(int) 38 => array(
'species' => 'vca',
'common_name' => 'Volvox carteri',
'tax_id' => '3067'
)
),
'all_species' => array(
'atr' => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333'
),
'ath' => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702'
),
'acg' => array(
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'tax_id' => '763042'
),
'aan' => array(
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'tax_id' => '44056'
),
'apr' => array(
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'tax_id' => '3075'
),
'bprrcc1105' => array(
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'tax_id' => '41875'
),
'cel' => array(
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'tax_id' => '6239'
),
'cre' => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055'
),
'cnc64a' => array(
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'tax_id' => '310507'
),
'ccr' => array(
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'tax_id' => '2769'
),
'cvu' => array(
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'tax_id' => '574566'
),
'cme' => array(
'species' => 'cme',
'common_name' => 'Cyanidioschyzon merolae',
'tax_id' => '45157'
),
'ddi' => array(
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'tax_id' => '44689'
),
'drm' => array(
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'tax_id' => '7227'
),
'esi' => array(
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'tax_id' => '2880'
),
'emh' => array(
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'tax_id' => '280463'
),
'fcy' => array(
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'tax_id' => '186039'
),
'gsu' => array(
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'tax_id' => '130081'
),
'hsp' => array(
'species' => 'hsp',
'common_name' => 'Helicosporidium sp. ',
'tax_id' => '145475'
),
'hom' => array(
'species' => 'hom',
'common_name' => 'Homo sapiens',
'tax_id' => '9606'
),
'mpu' => array(
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'tax_id' => '564608'
),
'mrcc299' => array(
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'tax_id' => '296587'
),
'mus' => array(
'species' => 'mus',
'common_name' => 'Mus musculus',
'tax_id' => '10090'
),
'nga' => array(
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'tax_id' => '72520'
),
'osa' => array(
'species' => 'osa',
'common_name' => 'Oryza sativa',
'tax_id' => '4530'
),
'olu' => array(
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'tax_id' => '242159'
),
'ome' => array(
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'tax_id' => '1486918'
),
'orcc809' => array(
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'tax_id' => '385169'
),
'ota' => array(
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'tax_id' => '70448'
),
'pte' => array(
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'tax_id' => '5888'
),
'ptri' => array(
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'tax_id' => '2850'
),
'ppa' => array(
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'tax_id' => '3218'
),
'phs' => array(
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'tax_id' => '67593'
),
'pse3' => array(
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'tax_id' => '1470871'
),
'prcc4223' => array(
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'tax_id' => '249344'
),
'sac' => array(
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'tax_id' => '4932'
),
'scp' => array(
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'tax_id' => '4896'
),
'tps' => array(
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'tax_id' => '35128'
),
'vca' => array(
'species' => 'vca',
'common_name' => 'Volvox carteri',
'tax_id' => '3067'
)
),
'gene_family_types_information' => array(
'HOMFAM' => array(
'id' => 'HOMFAM',
'name' => 'Homologous gene family',
'prefix' => 'HOM',
'gene_type' => 'coding',
'method' => '{}',
'ancestry' => 'homology',
'parent_id' => ''
),
'ORTHOFAM' => array(
'id' => 'ORTHOFAM',
'name' => 'Orthologous gene family',
'prefix' => 'ORTH',
'gene_type' => 'coding',
'method' => '{}',
'ancestry' => 'orthology',
'parent_id' => 'HOMFAM'
)
),
'gene_family_types_configuration' => array(),
'data_identifier' => 'ENSMUSG00000093862',
'data_type' => 'gene_id',
'allow_async_use' => true,
'gene_placeholder' => 'MP06G05470',
'gf_placeholder' => 'HOM03P001125',
'title_for_layout' => 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
)
$allowed_extra_sequences_types = array(
'aa' => 'Protein',
'dna' => 'DNA'
)
$allowed_editing_methods = array(
'column' => 'Positions only',
'row' => 'Genes only',
'column_row' => 'Positions and Genes',
'none' => 'No editing'
)
$allowed_tree_programs = array(
'fasttree' => 'FastTree',
'iqtree' => 'IQ-TREE (includes model testing)',
'raxml' => 'RAxML',
'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
'muscle' => 'MUSCLE',
'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
(int) 0 => 'all',
(int) 1 => (int) 20,
(int) 2 => (int) 10,
(int) 3 => (int) 5,
(int) 4 => (int) 1
)
$similarity_hits_genes = array(
'ENSMUSG00000093862' => array(
'gene_id' => 'ENSMUSG00000093862',
'e_value' => '0.0',
'bit_score' => '1786',
'alignment_length' => '858',
'identity_percentage' => '100.00',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ENSMUSG00000028233' => array(
'gene_id' => 'ENSMUSG00000028233',
'e_value' => '0.0',
'bit_score' => '1588',
'alignment_length' => '861',
'identity_percentage' => '91.41',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PP00092G00090' => array(
'gene_id' => 'PP00092G00090',
'e_value' => '9e-77',
'bit_score' => '270',
'alignment_length' => '205',
'identity_percentage' => '60.98',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AT1G45231' => array(
'gene_id' => 'AT1G45231',
'e_value' => '2e-72',
'bit_score' => '253',
'alignment_length' => '297',
'identity_percentage' => '47.81',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'emh729020' => array(
'gene_id' => 'emh729020',
'e_value' => '2e-69',
'bit_score' => '239',
'alignment_length' => '205',
'identity_percentage' => '58.05',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'FBgn0266195' => array(
'gene_id' => 'FBgn0266195',
'e_value' => '5e-69',
'bit_score' => '242',
'alignment_length' => '233',
'identity_percentage' => '49.79',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AT1G30550' => array(
'gene_id' => 'AT1G30550',
'e_value' => '1e-68',
'bit_score' => '241',
'alignment_length' => '203',
'identity_percentage' => '55.67',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ATR_00019G00550' => array(
'gene_id' => 'ATR_00019G00550',
'e_value' => '1e-68',
'bit_score' => '236',
'alignment_length' => '223',
'identity_percentage' => '52.91',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OS03G27930' => array(
'gene_id' => 'OS03G27930',
'e_value' => '5e-68',
'bit_score' => '245',
'alignment_length' => '204',
'identity_percentage' => '56.86',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ES0120G00110' => array(
'gene_id' => 'ES0120G00110',
'e_value' => '4e-67',
'bit_score' => '239',
'alignment_length' => '226',
'identity_percentage' => '51.77',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ATR_00003G02210' => array(
'gene_id' => 'ATR_00003G02210',
'e_value' => '4e-66',
'bit_score' => '240',
'alignment_length' => '202',
'identity_percentage' => '56.44',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'WBGene00011631' => array(
'gene_id' => 'WBGene00011631',
'e_value' => '2e-65',
'bit_score' => '234',
'alignment_length' => '227',
'identity_percentage' => '55.95',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'DDB_G0288547' => array(
'gene_id' => 'DDB_G0288547',
'e_value' => '9e-63',
'bit_score' => '220',
'alignment_length' => '212',
'identity_percentage' => '51.89',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'Naga_100003g58' => array(
'gene_id' => 'Naga_100003g58',
'e_value' => '1e-61',
'bit_score' => '221',
'alignment_length' => '203',
'identity_percentage' => '54.19',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AC00G95840' => array(
'gene_id' => 'AC00G95840',
'e_value' => '7e-60',
'bit_score' => '207',
'alignment_length' => '206',
'identity_percentage' => '50.00',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'phs121750' => array(
'gene_id' => 'phs121750',
'e_value' => '2e-58',
'bit_score' => '209',
'alignment_length' => '206',
'identity_percentage' => '50.00',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OS06G08800' => array(
'gene_id' => 'OS06G08800',
'e_value' => '2e-57',
'bit_score' => '204',
'alignment_length' => '206',
'identity_percentage' => '49.51',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ccr132780' => array(
'gene_id' => 'ccr132780',
'e_value' => '2e-56',
'bit_score' => '199',
'alignment_length' => '213',
'identity_percentage' => '48.36',
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'CNC64A_044G00080' => array(
'gene_id' => 'CNC64A_044G00080',
'e_value' => '1e-53',
'bit_score' => '196',
'alignment_length' => '214',
'identity_percentage' => '47.20',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OM_04G01940' => array(
'gene_id' => 'OM_04G01940',
'e_value' => '3e-53',
'bit_score' => '191',
'alignment_length' => '219',
'identity_percentage' => '44.29',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'CV00G61210' => array(
'gene_id' => 'CV00G61210',
'e_value' => '8e-50',
'bit_score' => '179',
'alignment_length' => '211',
'identity_percentage' => '44.08',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'RCC4223.19g00730' => array(
'gene_id' => 'RCC4223.19g00730',
'e_value' => '7e-49',
'bit_score' => '185',
'alignment_length' => '261',
'identity_percentage' => '41.38',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PI00G01490' => array(
'gene_id' => 'PI00G01490',
'e_value' => '2e-48',
'bit_score' => '184',
'alignment_length' => '306',
'identity_percentage' => '37.91',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'gsu74830' => array(
'gene_id' => 'gsu74830',
'e_value' => '9e-48',
'bit_score' => '175',
'alignment_length' => '230',
'identity_percentage' => '42.61',
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'CR06G11280' => array(
'gene_id' => 'CR06G11280',
'e_value' => '1e-46',
'bit_score' => '184',
'alignment_length' => '234',
'identity_percentage' => '42.74',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AP00G00630' => array(
'gene_id' => 'AP00G00630',
'e_value' => '1e-44',
'bit_score' => '175',
'alignment_length' => '242',
'identity_percentage' => '41.74',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'TP02G08210' => array(
'gene_id' => 'TP02G08210',
'e_value' => '3e-42',
'bit_score' => '160',
'alignment_length' => '247',
'identity_percentage' => '38.46',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'BPRRCC1105_14G03340' => array(
'gene_id' => 'BPRRCC1105_14G03340',
'e_value' => '1e-41',
'bit_score' => '156',
'alignment_length' => '183',
'identity_percentage' => '43.17',
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'SPAC2G11.15c' => array(
'gene_id' => 'SPAC2G11.15c',
'e_value' => '2e-41',
'bit_score' => '157',
'alignment_length' => '230',
'identity_percentage' => '39.13',
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'MRCC299_01G06910' => array(
'gene_id' => 'MRCC299_01G06910',
'e_value' => '1e-40',
'bit_score' => '160',
'alignment_length' => '247',
'identity_percentage' => '38.46',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OT_02G01350' => array(
'gene_id' => 'OT_02G01350',
'e_value' => '7e-39',
'bit_score' => '149',
'alignment_length' => '214',
'identity_percentage' => '38.79',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'MP02G06160' => array(
'gene_id' => 'MP02G06160',
'e_value' => '1e-37',
'bit_score' => '149',
'alignment_length' => '254',
'identity_percentage' => '35.43',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PTI_22G00250' => array(
'gene_id' => 'PTI_22G00250',
'e_value' => '4e-34',
'bit_score' => '141',
'alignment_length' => '308',
'identity_percentage' => '32.79',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P064266'
)
),
'CM19G03870' => array(
'gene_id' => 'CM19G03870',
'e_value' => '1e-33',
'bit_score' => '136',
'alignment_length' => '213',
'identity_percentage' => '38.03',
'species' => 'cme',
'common_name' => 'Cyanidioschyzon merolae',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'FC009G01340' => array(
'gene_id' => 'FC009G01340',
'e_value' => '5e-33',
'bit_score' => '134',
'alignment_length' => '229',
'identity_percentage' => '39.30',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AA0018G01160' => array(
'gene_id' => 'AA0018G01160',
'e_value' => '1e-31',
'bit_score' => '124',
'alignment_length' => '102',
'identity_percentage' => '54.90',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'YPL157W' => array(
'gene_id' => 'YPL157W',
'e_value' => '7e-29',
'bit_score' => '123',
'alignment_length' => '181',
'identity_percentage' => '38.67',
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'pte317770' => array(
'gene_id' => 'pte317770',
'e_value' => '1e-28',
'bit_score' => '121',
'alignment_length' => '216',
'identity_percentage' => '32.41',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PTI_22G00920' => array(
'gene_id' => 'PTI_22G00920',
'e_value' => '3e-27',
'bit_score' => '119',
'alignment_length' => '172',
'identity_percentage' => '41.28',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'pte644480' => array(
'gene_id' => 'pte644480',
'e_value' => '1e-25',
'bit_score' => '112',
'alignment_length' => '231',
'identity_percentage' => '32.03',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'pte492450' => array(
'gene_id' => 'pte492450',
'e_value' => '3e-24',
'bit_score' => '108',
'alignment_length' => '231',
'identity_percentage' => '30.74',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'TP07G02910' => array(
'gene_id' => 'TP07G02910',
'e_value' => '8e-22',
'bit_score' => '97.8',
'alignment_length' => '125',
'identity_percentage' => '44.00',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P079127'
)
),
'OL02G04740' => array(
'gene_id' => 'OL02G04740',
'e_value' => '1e-18',
'bit_score' => '87.8',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'FC004G05310' => array(
'gene_id' => 'FC004G05310',
'e_value' => '2e-18',
'bit_score' => '91.3',
'alignment_length' => '180',
'identity_percentage' => '35.00',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P064266'
)
),
'ORCC809_02G02560' => array(
'gene_id' => 'ORCC809_02G02560',
'e_value' => '4e-17',
'bit_score' => '82.8',
'alignment_length' => '79',
'identity_percentage' => '50.63',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'pte690930' => array(
'gene_id' => 'pte690930',
'e_value' => '3e-15',
'bit_score' => '83.2',
'alignment_length' => '196',
'identity_percentage' => '30.61',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P016463',
'ORTHOFAM' => 'ORTHO03P047521'
)
),
'pte615620' => array(
'gene_id' => 'pte615620',
'e_value' => '7e-14',
'bit_score' => '79.0',
'alignment_length' => '201',
'identity_percentage' => '29.85',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P016463',
'ORTHOFAM' => 'ORTHO03P047521'
)
),
'Naga_100031g18' => array(
'gene_id' => 'Naga_100031g18',
'e_value' => '7e-14',
'bit_score' => '77.8',
'alignment_length' => '160',
'identity_percentage' => '29.38',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P028903'
)
),
'phs302960' => array(
'gene_id' => 'phs302960',
'e_value' => '5e-10',
'bit_score' => '67.0',
'alignment_length' => '138',
'identity_percentage' => '32.61',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P028903'
)
),
'ccr191460' => array(
'gene_id' => 'ccr191460',
'e_value' => '3e-07',
'bit_score' => '57.0',
'alignment_length' => '116',
'identity_percentage' => '33.62',
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'gf' => array(
'HOMFAM' => 'HOM03P002616',
'ORTHOFAM' => 'ORTHO03P001814'
)
),
'ES0387G00030' => array(
'gene_id' => 'ES0387G00030',
'e_value' => '1e-06',
'bit_score' => '53.1',
'alignment_length' => '124',
'identity_percentage' => '30.65',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P013338',
'ORTHOFAM' => 'ORTHO03P028903'
)
)
)
$similarity_hits_species = array(
'mus' => array(
(int) 0 => 'ENSMUSG00000093862',
(int) 1 => 'ENSMUSG00000028233'
),
'ppa' => array(
(int) 0 => 'PP00092G00090'
),
'ath' => array(
(int) 0 => 'AT1G45231',
(int) 1 => 'AT1G30550'
),
'emh' => array(
(int) 0 => 'emh729020'
),
'drm' => array(
(int) 0 => 'FBgn0266195'
),
'atr' => array(
(int) 0 => 'ATR_00019G00550',
(int) 1 => 'ATR_00003G02210'
),
'osa' => array(
(int) 0 => 'OS03G27930',
(int) 1 => 'OS06G08800'
),
'esi' => array(
(int) 0 => 'ES0120G00110',
(int) 1 => 'ES0387G00030'
),
'cel' => array(
(int) 0 => 'WBGene00011631'
),
'ddi' => array(
(int) 0 => 'DDB_G0288547'
),
'nga' => array(
(int) 0 => 'Naga_100003g58',
(int) 1 => 'Naga_100031g18'
),
'acg' => array(
(int) 0 => 'AC00G95840'
),
'phs' => array(
(int) 0 => 'phs121750',
(int) 1 => 'phs302960'
),
'ccr' => array(
(int) 0 => 'ccr132780',
(int) 1 => 'ccr191460'
),
'ome' => array(
(int) 0 => 'OM_04G01940'
),
'cvu' => array(
(int) 0 => 'CV00G61210'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.19g00730'
),
'pse3' => array(
(int) 0 => 'PI00G01490'
),
'gsu' => array(
(int) 0 => 'gsu74830'
),
'cre' => array(
(int) 0 => 'CR06G11280'
),
'apr' => array(
(int) 0 => 'AP00G00630'
),
'tps' => array(
(int) 0 => 'TP02G08210',
(int) 1 => 'TP07G02910'
),
'bprrcc1105' => array(
(int) 0 => 'BPRRCC1105_14G03340'
),
'scp' => array(
(int) 0 => 'SPAC2G11.15c'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_01G06910'
),
'ota' => array(
(int) 0 => 'OT_02G01350'
),
'mpu' => array(
(int) 0 => 'MP02G06160'
),
'ptri' => array(
(int) 0 => 'PTI_22G00250',
(int) 1 => 'PTI_22G00920'
),
'cme' => array(
(int) 0 => 'CM19G03870'
),
'fcy' => array(
(int) 0 => 'FC009G01340',
(int) 1 => 'FC004G05310'
),
'aan' => array(
(int) 0 => 'AA0018G01160'
),
'sac' => array(
(int) 0 => 'YPL157W'
),
'pte' => array(
(int) 0 => 'pte317770',
(int) 1 => 'pte644480',
(int) 2 => 'pte492450',
(int) 3 => 'pte690930',
(int) 4 => 'pte615620'
),
'olu' => array(
(int) 0 => 'OL02G04740'
),
'orcc809' => array(
(int) 0 => 'ORCC809_02G02560'
)
)
$gene_id = 'ENSMUSG00000093862'
$all_species_index = array(
(int) 0 => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333'
),
(int) 1 => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702'
),
(int) 2 => array(
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'tax_id' => '763042'
),
(int) 3 => array(
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'tax_id' => '44056'
),
(int) 4 => array(
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'tax_id' => '3075'
),
(int) 5 => array(
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'tax_id' => '41875'
),
(int) 6 => array(
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'tax_id' => '6239'
),
(int) 7 => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055'
),
(int) 8 => array(
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'tax_id' => '310507'
),
(int) 9 => array(
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'tax_id' => '2769'
),
(int) 10 => array(
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'tax_id' => '574566'
),
(int) 11 => array(
'species' => 'cme',
'common_name' => 'Cyanidioschyzon merolae',
'tax_id' => '45157'
),
(int) 12 => array(
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'tax_id' => '44689'
),
(int) 13 => array(
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'tax_id' => '7227'
),
(int) 14 => array(
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'tax_id' => '2880'
),
(int) 15 => array(
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'tax_id' => '280463'
),
(int) 16 => array(
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'tax_id' => '186039'
),
(int) 17 => array(
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'tax_id' => '130081'
),
(int) 18 => array(
'species' => 'hsp',
'common_name' => 'Helicosporidium sp. ',
'tax_id' => '145475'
),
(int) 19 => array(
'species' => 'hom',
'common_name' => 'Homo sapiens',
'tax_id' => '9606'
),
(int) 20 => array(
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'tax_id' => '564608'
),
(int) 21 => array(
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'tax_id' => '296587'
),
(int) 22 => array(
'species' => 'mus',
'common_name' => 'Mus musculus',
'tax_id' => '10090'
),
(int) 23 => array(
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'tax_id' => '72520'
),
(int) 24 => array(
'species' => 'osa',
'common_name' => 'Oryza sativa',
'tax_id' => '4530'
),
(int) 25 => array(
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'tax_id' => '242159'
),
(int) 26 => array(
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'tax_id' => '1486918'
),
(int) 27 => array(
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'tax_id' => '385169'
),
(int) 28 => array(
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'tax_id' => '70448'
),
(int) 29 => array(
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'tax_id' => '5888'
),
(int) 30 => array(
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'tax_id' => '2850'
),
(int) 31 => array(
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'tax_id' => '3218'
),
(int) 32 => array(
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'tax_id' => '67593'
),
(int) 33 => array(
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'tax_id' => '1470871'
),
(int) 34 => array(
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'tax_id' => '249344'
),
(int) 35 => array(
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'tax_id' => '4932'
),
(int) 36 => array(
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'tax_id' => '4896'
),
(int) 37 => array(
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'tax_id' => '35128'
),
(int) 38 => array(
'species' => 'vca',
'common_name' => 'Volvox carteri',
'tax_id' => '3067'
)
)
$all_species = array(
'atr' => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333'
),
'ath' => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702'
),
'acg' => array(
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'tax_id' => '763042'
),
'aan' => array(
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'tax_id' => '44056'
),
'apr' => array(
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'tax_id' => '3075'
),
'bprrcc1105' => array(
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'tax_id' => '41875'
),
'cel' => array(
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'tax_id' => '6239'
),
'cre' => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055'
),
'cnc64a' => array(
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'tax_id' => '310507'
),
'ccr' => array(
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'tax_id' => '2769'
),
'cvu' => array(
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'tax_id' => '574566'
),
'cme' => array(
'species' => 'cme',
'common_name' => 'Cyanidioschyzon merolae',
'tax_id' => '45157'
),
'ddi' => array(
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'tax_id' => '44689'
),
'drm' => array(
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'tax_id' => '7227'
),
'esi' => array(
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'tax_id' => '2880'
),
'emh' => array(
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'tax_id' => '280463'
),
'fcy' => array(
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'tax_id' => '186039'
),
'gsu' => array(
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'tax_id' => '130081'
),
'hsp' => array(
'species' => 'hsp',
'common_name' => 'Helicosporidium sp. ',
'tax_id' => '145475'
),
'hom' => array(
'species' => 'hom',
'common_name' => 'Homo sapiens',
'tax_id' => '9606'
),
'mpu' => array(
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'tax_id' => '564608'
),
'mrcc299' => array(
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'tax_id' => '296587'
),
'mus' => array(
'species' => 'mus',
'common_name' => 'Mus musculus',
'tax_id' => '10090'
),
'nga' => array(
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'tax_id' => '72520'
),
'osa' => array(
'species' => 'osa',
'common_name' => 'Oryza sativa',
'tax_id' => '4530'
),
'olu' => array(
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'tax_id' => '242159'
),
'ome' => array(
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'tax_id' => '1486918'
),
'orcc809' => array(
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'tax_id' => '385169'
),
'ota' => array(
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'tax_id' => '70448'
),
'pte' => array(
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'tax_id' => '5888'
),
'ptri' => array(
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'tax_id' => '2850'
),
'ppa' => array(
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'tax_id' => '3218'
),
'phs' => array(
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'tax_id' => '67593'
),
'pse3' => array(
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'tax_id' => '1470871'
),
'prcc4223' => array(
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'tax_id' => '249344'
),
'sac' => array(
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'tax_id' => '4932'
),
'scp' => array(
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'tax_id' => '4896'
),
'tps' => array(
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'tax_id' => '35128'
),
'vca' => array(
'species' => 'vca',
'common_name' => 'Volvox carteri',
'tax_id' => '3067'
)
)
$gene_family_types_information = array(
'HOMFAM' => array(
'id' => 'HOMFAM',
'name' => 'Homologous gene family',
'prefix' => 'HOM',
'gene_type' => 'coding',
'method' => '{}',
'ancestry' => 'homology',
'parent_id' => ''
),
'ORTHOFAM' => array(
'id' => 'ORTHOFAM',
'name' => 'Orthologous gene family',
'prefix' => 'ORTH',
'gene_type' => 'coding',
'method' => '{}',
'ancestry' => 'orthology',
'parent_id' => 'HOMFAM'
)
)
$gene_family_types_configuration = array()
$data_identifier = 'ENSMUSG00000093862'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'MP06G05470'
$gf_placeholder = 'HOM03P001125'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
'gene_id' => 'CNC64A_044G00080',
'e_value' => '1e-53',
'bit_score' => '196',
'alignment_length' => '214',
'identity_percentage' => '47.20',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
)
$checked = null
$similarity_hit_gene = 'CNC64A_044G00080'
include - APP/View/Analysis/custom_tree_creation.ctp, line 169
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 146
Notice (8): Undefined index: common_name [APP/View/Analysis/custom_tree_creation.ctp, line 169]Code Context echo "<td><input type='checkbox' name='selected_genes[]' value='".$similarity_hit['gene_id']."' ".$checked." /></td>\n";
echo "<td>".$this->Html->link($similarity_hit_gene,array("controller"=>"genes","action"=>"view",$similarity_hit_gene),array("target"=>"_blank"))."</td>\n";
echo "<td>".$this->Html->link($similarity_hit['common_name'],array("controller"=>"organism","action"=>"view",urlencode($similarity_hit['common_name'])))."</td>\n";
$viewFile = '/xtras/group/biocomp/plaza/versions/plaza_pico_03/app/View/Analysis/custom_tree_creation.ctp'
$dataForView = array(
'allowed_extra_sequences_types' => array(
'aa' => 'Protein',
'dna' => 'DNA'
),
'allowed_editing_methods' => array(
'column' => 'Positions only',
'row' => 'Genes only',
'column_row' => 'Positions and Genes',
'none' => 'No editing'
),
'allowed_tree_programs' => array(
'fasttree' => 'FastTree',
'iqtree' => 'IQ-TREE (includes model testing)',
'raxml' => 'RAxML',
'phyml' => 'PhyML'
),
'allowed_msa_programs' => array(
'muscle' => 'MUSCLE',
'mafft' => 'MAFFT'
),
'allowed_number_blasthits' => array(
(int) 0 => 'all',
(int) 1 => (int) 20,
(int) 2 => (int) 10,
(int) 3 => (int) 5,
(int) 4 => (int) 1
),
'similarity_hits_genes' => array(
'ENSMUSG00000093862' => array(
'gene_id' => 'ENSMUSG00000093862',
'e_value' => '0.0',
'bit_score' => '1786',
'alignment_length' => '858',
'identity_percentage' => '100.00',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
[maximum depth reached]
)
),
'ENSMUSG00000028233' => array(
'gene_id' => 'ENSMUSG00000028233',
'e_value' => '0.0',
'bit_score' => '1588',
'alignment_length' => '861',
'identity_percentage' => '91.41',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
[maximum depth reached]
)
),
'PP00092G00090' => array(
'gene_id' => 'PP00092G00090',
'e_value' => '9e-77',
'bit_score' => '270',
'alignment_length' => '205',
'identity_percentage' => '60.98',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'AT1G45231' => array(
'gene_id' => 'AT1G45231',
'e_value' => '2e-72',
'bit_score' => '253',
'alignment_length' => '297',
'identity_percentage' => '47.81',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'emh729020' => array(
'gene_id' => 'emh729020',
'e_value' => '2e-69',
'bit_score' => '239',
'alignment_length' => '205',
'identity_percentage' => '58.05',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'FBgn0266195' => array(
'gene_id' => 'FBgn0266195',
'e_value' => '5e-69',
'bit_score' => '242',
'alignment_length' => '233',
'identity_percentage' => '49.79',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
[maximum depth reached]
)
),
'AT1G30550' => array(
'gene_id' => 'AT1G30550',
'e_value' => '1e-68',
'bit_score' => '241',
'alignment_length' => '203',
'identity_percentage' => '55.67',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00019G00550' => array(
'gene_id' => 'ATR_00019G00550',
'e_value' => '1e-68',
'bit_score' => '236',
'alignment_length' => '223',
'identity_percentage' => '52.91',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'OS03G27930' => array(
'gene_id' => 'OS03G27930',
'e_value' => '5e-68',
'bit_score' => '245',
'alignment_length' => '204',
'identity_percentage' => '56.86',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'ES0120G00110' => array(
'gene_id' => 'ES0120G00110',
'e_value' => '4e-67',
'bit_score' => '239',
'alignment_length' => '226',
'identity_percentage' => '51.77',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00003G02210' => array(
'gene_id' => 'ATR_00003G02210',
'e_value' => '4e-66',
'bit_score' => '240',
'alignment_length' => '202',
'identity_percentage' => '56.44',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'WBGene00011631' => array(
'gene_id' => 'WBGene00011631',
'e_value' => '2e-65',
'bit_score' => '234',
'alignment_length' => '227',
'identity_percentage' => '55.95',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
[maximum depth reached]
)
),
'DDB_G0288547' => array(
'gene_id' => 'DDB_G0288547',
'e_value' => '9e-63',
'bit_score' => '220',
'alignment_length' => '212',
'identity_percentage' => '51.89',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
[maximum depth reached]
)
),
'Naga_100003g58' => array(
'gene_id' => 'Naga_100003g58',
'e_value' => '1e-61',
'bit_score' => '221',
'alignment_length' => '203',
'identity_percentage' => '54.19',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
[maximum depth reached]
)
),
'AC00G95840' => array(
'gene_id' => 'AC00G95840',
'e_value' => '7e-60',
'bit_score' => '207',
'alignment_length' => '206',
'identity_percentage' => '50.00',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
[maximum depth reached]
)
),
'phs121750' => array(
'gene_id' => 'phs121750',
'e_value' => '2e-58',
'bit_score' => '209',
'alignment_length' => '206',
'identity_percentage' => '50.00',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
[maximum depth reached]
)
),
'OS06G08800' => array(
'gene_id' => 'OS06G08800',
'e_value' => '2e-57',
'bit_score' => '204',
'alignment_length' => '206',
'identity_percentage' => '49.51',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'ccr132780' => array(
'gene_id' => 'ccr132780',
'e_value' => '2e-56',
'bit_score' => '199',
'alignment_length' => '213',
'identity_percentage' => '48.36',
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_044G00080' => array(
'gene_id' => 'CNC64A_044G00080',
'e_value' => '1e-53',
'bit_score' => '196',
'alignment_length' => '214',
'identity_percentage' => '47.20',
'gf' => array(
[maximum depth reached]
)
),
'OM_04G01940' => array(
'gene_id' => 'OM_04G01940',
'e_value' => '3e-53',
'bit_score' => '191',
'alignment_length' => '219',
'identity_percentage' => '44.29',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
[maximum depth reached]
)
),
'CV00G61210' => array(
'gene_id' => 'CV00G61210',
'e_value' => '8e-50',
'bit_score' => '179',
'alignment_length' => '211',
'identity_percentage' => '44.08',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.19g00730' => array(
'gene_id' => 'RCC4223.19g00730',
'e_value' => '7e-49',
'bit_score' => '185',
'alignment_length' => '261',
'identity_percentage' => '41.38',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G01490' => array(
'gene_id' => 'PI00G01490',
'e_value' => '2e-48',
'bit_score' => '184',
'alignment_length' => '306',
'identity_percentage' => '37.91',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'gsu74830' => array(
'gene_id' => 'gsu74830',
'e_value' => '9e-48',
'bit_score' => '175',
'alignment_length' => '230',
'identity_percentage' => '42.61',
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'gf' => array(
[maximum depth reached]
)
),
'CR06G11280' => array(
'gene_id' => 'CR06G11280',
'e_value' => '1e-46',
'bit_score' => '184',
'alignment_length' => '234',
'identity_percentage' => '42.74',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'AP00G00630' => array(
'gene_id' => 'AP00G00630',
'e_value' => '1e-44',
'bit_score' => '175',
'alignment_length' => '242',
'identity_percentage' => '41.74',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'TP02G08210' => array(
'gene_id' => 'TP02G08210',
'e_value' => '3e-42',
'bit_score' => '160',
'alignment_length' => '247',
'identity_percentage' => '38.46',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
[maximum depth reached]
)
),
'BPRRCC1105_14G03340' => array(
'gene_id' => 'BPRRCC1105_14G03340',
'e_value' => '1e-41',
'bit_score' => '156',
'alignment_length' => '183',
'identity_percentage' => '43.17',
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'gf' => array(
[maximum depth reached]
)
),
'SPAC2G11.15c' => array(
'gene_id' => 'SPAC2G11.15c',
'e_value' => '2e-41',
'bit_score' => '157',
'alignment_length' => '230',
'identity_percentage' => '39.13',
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'gf' => array(
[maximum depth reached]
)
),
'MRCC299_01G06910' => array(
'gene_id' => 'MRCC299_01G06910',
'e_value' => '1e-40',
'bit_score' => '160',
'alignment_length' => '247',
'identity_percentage' => '38.46',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
[maximum depth reached]
)
),
'OT_02G01350' => array(
'gene_id' => 'OT_02G01350',
'e_value' => '7e-39',
'bit_score' => '149',
'alignment_length' => '214',
'identity_percentage' => '38.79',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
[maximum depth reached]
)
),
'MP02G06160' => array(
'gene_id' => 'MP02G06160',
'e_value' => '1e-37',
'bit_score' => '149',
'alignment_length' => '254',
'identity_percentage' => '35.43',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
[maximum depth reached]
)
),
'PTI_22G00250' => array(
'gene_id' => 'PTI_22G00250',
'e_value' => '4e-34',
'bit_score' => '141',
'alignment_length' => '308',
'identity_percentage' => '32.79',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'CM19G03870' => array(
'gene_id' => 'CM19G03870',
'e_value' => '1e-33',
'bit_score' => '136',
'alignment_length' => '213',
'identity_percentage' => '38.03',
'species' => 'cme',
'common_name' => 'Cyanidioschyzon merolae',
'gf' => array(
[maximum depth reached]
)
),
'FC009G01340' => array(
'gene_id' => 'FC009G01340',
'e_value' => '5e-33',
'bit_score' => '134',
'alignment_length' => '229',
'identity_percentage' => '39.30',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
[maximum depth reached]
)
),
'AA0018G01160' => array(
'gene_id' => 'AA0018G01160',
'e_value' => '1e-31',
'bit_score' => '124',
'alignment_length' => '102',
'identity_percentage' => '54.90',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'YPL157W' => array(
'gene_id' => 'YPL157W',
'e_value' => '7e-29',
'bit_score' => '123',
'alignment_length' => '181',
'identity_percentage' => '38.67',
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'gf' => array(
[maximum depth reached]
)
),
'pte317770' => array(
'gene_id' => 'pte317770',
'e_value' => '1e-28',
'bit_score' => '121',
'alignment_length' => '216',
'identity_percentage' => '32.41',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'PTI_22G00920' => array(
'gene_id' => 'PTI_22G00920',
'e_value' => '3e-27',
'bit_score' => '119',
'alignment_length' => '172',
'identity_percentage' => '41.28',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'pte644480' => array(
'gene_id' => 'pte644480',
'e_value' => '1e-25',
'bit_score' => '112',
'alignment_length' => '231',
'identity_percentage' => '32.03',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'pte492450' => array(
'gene_id' => 'pte492450',
'e_value' => '3e-24',
'bit_score' => '108',
'alignment_length' => '231',
'identity_percentage' => '30.74',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'TP07G02910' => array(
'gene_id' => 'TP07G02910',
'e_value' => '8e-22',
'bit_score' => '97.8',
'alignment_length' => '125',
'identity_percentage' => '44.00',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
[maximum depth reached]
)
),
'OL02G04740' => array(
'gene_id' => 'OL02G04740',
'e_value' => '1e-18',
'bit_score' => '87.8',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
[maximum depth reached]
)
),
'FC004G05310' => array(
'gene_id' => 'FC004G05310',
'e_value' => '2e-18',
'bit_score' => '91.3',
'alignment_length' => '180',
'identity_percentage' => '35.00',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
[maximum depth reached]
)
),
'ORCC809_02G02560' => array(
'gene_id' => 'ORCC809_02G02560',
'e_value' => '4e-17',
'bit_score' => '82.8',
'alignment_length' => '79',
'identity_percentage' => '50.63',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
[maximum depth reached]
)
),
'pte690930' => array(
'gene_id' => 'pte690930',
'e_value' => '3e-15',
'bit_score' => '83.2',
'alignment_length' => '196',
'identity_percentage' => '30.61',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'pte615620' => array(
'gene_id' => 'pte615620',
'e_value' => '7e-14',
'bit_score' => '79.0',
'alignment_length' => '201',
'identity_percentage' => '29.85',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'Naga_100031g18' => array(
'gene_id' => 'Naga_100031g18',
'e_value' => '7e-14',
'bit_score' => '77.8',
'alignment_length' => '160',
'identity_percentage' => '29.38',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
[maximum depth reached]
)
),
'phs302960' => array(
'gene_id' => 'phs302960',
'e_value' => '5e-10',
'bit_score' => '67.0',
'alignment_length' => '138',
'identity_percentage' => '32.61',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
[maximum depth reached]
)
),
'ccr191460' => array(
'gene_id' => 'ccr191460',
'e_value' => '3e-07',
'bit_score' => '57.0',
'alignment_length' => '116',
'identity_percentage' => '33.62',
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'gf' => array(
[maximum depth reached]
)
),
'ES0387G00030' => array(
'gene_id' => 'ES0387G00030',
'e_value' => '1e-06',
'bit_score' => '53.1',
'alignment_length' => '124',
'identity_percentage' => '30.65',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
)
),
'similarity_hits_species' => array(
'mus' => array(
(int) 0 => 'ENSMUSG00000093862',
(int) 1 => 'ENSMUSG00000028233'
),
'ppa' => array(
(int) 0 => 'PP00092G00090'
),
'ath' => array(
(int) 0 => 'AT1G45231',
(int) 1 => 'AT1G30550'
),
'emh' => array(
(int) 0 => 'emh729020'
),
'drm' => array(
(int) 0 => 'FBgn0266195'
),
'atr' => array(
(int) 0 => 'ATR_00019G00550',
(int) 1 => 'ATR_00003G02210'
),
'osa' => array(
(int) 0 => 'OS03G27930',
(int) 1 => 'OS06G08800'
),
'esi' => array(
(int) 0 => 'ES0120G00110',
(int) 1 => 'ES0387G00030'
),
'cel' => array(
(int) 0 => 'WBGene00011631'
),
'ddi' => array(
(int) 0 => 'DDB_G0288547'
),
'nga' => array(
(int) 0 => 'Naga_100003g58',
(int) 1 => 'Naga_100031g18'
),
'acg' => array(
(int) 0 => 'AC00G95840'
),
'phs' => array(
(int) 0 => 'phs121750',
(int) 1 => 'phs302960'
),
'ccr' => array(
(int) 0 => 'ccr132780',
(int) 1 => 'ccr191460'
),
'ome' => array(
(int) 0 => 'OM_04G01940'
),
'cvu' => array(
(int) 0 => 'CV00G61210'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.19g00730'
),
'pse3' => array(
(int) 0 => 'PI00G01490'
),
'gsu' => array(
(int) 0 => 'gsu74830'
),
'cre' => array(
(int) 0 => 'CR06G11280'
),
'apr' => array(
(int) 0 => 'AP00G00630'
),
'tps' => array(
(int) 0 => 'TP02G08210',
(int) 1 => 'TP07G02910'
),
'bprrcc1105' => array(
(int) 0 => 'BPRRCC1105_14G03340'
),
'scp' => array(
(int) 0 => 'SPAC2G11.15c'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_01G06910'
),
'ota' => array(
(int) 0 => 'OT_02G01350'
),
'mpu' => array(
(int) 0 => 'MP02G06160'
),
'ptri' => array(
(int) 0 => 'PTI_22G00250',
(int) 1 => 'PTI_22G00920'
),
'cme' => array(
(int) 0 => 'CM19G03870'
),
'fcy' => array(
(int) 0 => 'FC009G01340',
(int) 1 => 'FC004G05310'
),
'aan' => array(
(int) 0 => 'AA0018G01160'
),
'sac' => array(
(int) 0 => 'YPL157W'
),
'pte' => array(
(int) 0 => 'pte317770',
(int) 1 => 'pte644480',
(int) 2 => 'pte492450',
(int) 3 => 'pte690930',
(int) 4 => 'pte615620'
),
'olu' => array(
(int) 0 => 'OL02G04740'
),
'orcc809' => array(
(int) 0 => 'ORCC809_02G02560'
)
),
'gene_id' => 'ENSMUSG00000093862',
'all_species_index' => array(
(int) 0 => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333'
),
(int) 1 => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702'
),
(int) 2 => array(
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'tax_id' => '763042'
),
(int) 3 => array(
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'tax_id' => '44056'
),
(int) 4 => array(
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'tax_id' => '3075'
),
(int) 5 => array(
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'tax_id' => '41875'
),
(int) 6 => array(
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'tax_id' => '6239'
),
(int) 7 => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055'
),
(int) 8 => array(
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'tax_id' => '310507'
),
(int) 9 => array(
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'tax_id' => '2769'
),
(int) 10 => array(
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'tax_id' => '574566'
),
(int) 11 => array(
'species' => 'cme',
'common_name' => 'Cyanidioschyzon merolae',
'tax_id' => '45157'
),
(int) 12 => array(
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'tax_id' => '44689'
),
(int) 13 => array(
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'tax_id' => '7227'
),
(int) 14 => array(
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'tax_id' => '2880'
),
(int) 15 => array(
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'tax_id' => '280463'
),
(int) 16 => array(
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'tax_id' => '186039'
),
(int) 17 => array(
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'tax_id' => '130081'
),
(int) 18 => array(
'species' => 'hsp',
'common_name' => 'Helicosporidium sp. ',
'tax_id' => '145475'
),
(int) 19 => array(
'species' => 'hom',
'common_name' => 'Homo sapiens',
'tax_id' => '9606'
),
(int) 20 => array(
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'tax_id' => '564608'
),
(int) 21 => array(
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'tax_id' => '296587'
),
(int) 22 => array(
'species' => 'mus',
'common_name' => 'Mus musculus',
'tax_id' => '10090'
),
(int) 23 => array(
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'tax_id' => '72520'
),
(int) 24 => array(
'species' => 'osa',
'common_name' => 'Oryza sativa',
'tax_id' => '4530'
),
(int) 25 => array(
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'tax_id' => '242159'
),
(int) 26 => array(
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'tax_id' => '1486918'
),
(int) 27 => array(
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'tax_id' => '385169'
),
(int) 28 => array(
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'tax_id' => '70448'
),
(int) 29 => array(
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'tax_id' => '5888'
),
(int) 30 => array(
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'tax_id' => '2850'
),
(int) 31 => array(
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'tax_id' => '3218'
),
(int) 32 => array(
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'tax_id' => '67593'
),
(int) 33 => array(
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'tax_id' => '1470871'
),
(int) 34 => array(
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'tax_id' => '249344'
),
(int) 35 => array(
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'tax_id' => '4932'
),
(int) 36 => array(
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'tax_id' => '4896'
),
(int) 37 => array(
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'tax_id' => '35128'
),
(int) 38 => array(
'species' => 'vca',
'common_name' => 'Volvox carteri',
'tax_id' => '3067'
)
),
'all_species' => array(
'atr' => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333'
),
'ath' => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702'
),
'acg' => array(
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'tax_id' => '763042'
),
'aan' => array(
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'tax_id' => '44056'
),
'apr' => array(
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'tax_id' => '3075'
),
'bprrcc1105' => array(
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'tax_id' => '41875'
),
'cel' => array(
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'tax_id' => '6239'
),
'cre' => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055'
),
'cnc64a' => array(
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'tax_id' => '310507'
),
'ccr' => array(
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'tax_id' => '2769'
),
'cvu' => array(
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'tax_id' => '574566'
),
'cme' => array(
'species' => 'cme',
'common_name' => 'Cyanidioschyzon merolae',
'tax_id' => '45157'
),
'ddi' => array(
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'tax_id' => '44689'
),
'drm' => array(
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'tax_id' => '7227'
),
'esi' => array(
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'tax_id' => '2880'
),
'emh' => array(
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'tax_id' => '280463'
),
'fcy' => array(
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'tax_id' => '186039'
),
'gsu' => array(
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'tax_id' => '130081'
),
'hsp' => array(
'species' => 'hsp',
'common_name' => 'Helicosporidium sp. ',
'tax_id' => '145475'
),
'hom' => array(
'species' => 'hom',
'common_name' => 'Homo sapiens',
'tax_id' => '9606'
),
'mpu' => array(
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'tax_id' => '564608'
),
'mrcc299' => array(
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'tax_id' => '296587'
),
'mus' => array(
'species' => 'mus',
'common_name' => 'Mus musculus',
'tax_id' => '10090'
),
'nga' => array(
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'tax_id' => '72520'
),
'osa' => array(
'species' => 'osa',
'common_name' => 'Oryza sativa',
'tax_id' => '4530'
),
'olu' => array(
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'tax_id' => '242159'
),
'ome' => array(
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'tax_id' => '1486918'
),
'orcc809' => array(
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'tax_id' => '385169'
),
'ota' => array(
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'tax_id' => '70448'
),
'pte' => array(
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'tax_id' => '5888'
),
'ptri' => array(
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'tax_id' => '2850'
),
'ppa' => array(
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'tax_id' => '3218'
),
'phs' => array(
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'tax_id' => '67593'
),
'pse3' => array(
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'tax_id' => '1470871'
),
'prcc4223' => array(
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'tax_id' => '249344'
),
'sac' => array(
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'tax_id' => '4932'
),
'scp' => array(
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'tax_id' => '4896'
),
'tps' => array(
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'tax_id' => '35128'
),
'vca' => array(
'species' => 'vca',
'common_name' => 'Volvox carteri',
'tax_id' => '3067'
)
),
'gene_family_types_information' => array(
'HOMFAM' => array(
'id' => 'HOMFAM',
'name' => 'Homologous gene family',
'prefix' => 'HOM',
'gene_type' => 'coding',
'method' => '{}',
'ancestry' => 'homology',
'parent_id' => ''
),
'ORTHOFAM' => array(
'id' => 'ORTHOFAM',
'name' => 'Orthologous gene family',
'prefix' => 'ORTH',
'gene_type' => 'coding',
'method' => '{}',
'ancestry' => 'orthology',
'parent_id' => 'HOMFAM'
)
),
'gene_family_types_configuration' => array(),
'data_identifier' => 'ENSMUSG00000093862',
'data_type' => 'gene_id',
'allow_async_use' => true,
'gene_placeholder' => 'MP06G05470',
'gf_placeholder' => 'HOM03P001125',
'title_for_layout' => 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
)
$allowed_extra_sequences_types = array(
'aa' => 'Protein',
'dna' => 'DNA'
)
$allowed_editing_methods = array(
'column' => 'Positions only',
'row' => 'Genes only',
'column_row' => 'Positions and Genes',
'none' => 'No editing'
)
$allowed_tree_programs = array(
'fasttree' => 'FastTree',
'iqtree' => 'IQ-TREE (includes model testing)',
'raxml' => 'RAxML',
'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
'muscle' => 'MUSCLE',
'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
(int) 0 => 'all',
(int) 1 => (int) 20,
(int) 2 => (int) 10,
(int) 3 => (int) 5,
(int) 4 => (int) 1
)
$similarity_hits_genes = array(
'ENSMUSG00000093862' => array(
'gene_id' => 'ENSMUSG00000093862',
'e_value' => '0.0',
'bit_score' => '1786',
'alignment_length' => '858',
'identity_percentage' => '100.00',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ENSMUSG00000028233' => array(
'gene_id' => 'ENSMUSG00000028233',
'e_value' => '0.0',
'bit_score' => '1588',
'alignment_length' => '861',
'identity_percentage' => '91.41',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PP00092G00090' => array(
'gene_id' => 'PP00092G00090',
'e_value' => '9e-77',
'bit_score' => '270',
'alignment_length' => '205',
'identity_percentage' => '60.98',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AT1G45231' => array(
'gene_id' => 'AT1G45231',
'e_value' => '2e-72',
'bit_score' => '253',
'alignment_length' => '297',
'identity_percentage' => '47.81',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'emh729020' => array(
'gene_id' => 'emh729020',
'e_value' => '2e-69',
'bit_score' => '239',
'alignment_length' => '205',
'identity_percentage' => '58.05',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'FBgn0266195' => array(
'gene_id' => 'FBgn0266195',
'e_value' => '5e-69',
'bit_score' => '242',
'alignment_length' => '233',
'identity_percentage' => '49.79',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AT1G30550' => array(
'gene_id' => 'AT1G30550',
'e_value' => '1e-68',
'bit_score' => '241',
'alignment_length' => '203',
'identity_percentage' => '55.67',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ATR_00019G00550' => array(
'gene_id' => 'ATR_00019G00550',
'e_value' => '1e-68',
'bit_score' => '236',
'alignment_length' => '223',
'identity_percentage' => '52.91',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OS03G27930' => array(
'gene_id' => 'OS03G27930',
'e_value' => '5e-68',
'bit_score' => '245',
'alignment_length' => '204',
'identity_percentage' => '56.86',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ES0120G00110' => array(
'gene_id' => 'ES0120G00110',
'e_value' => '4e-67',
'bit_score' => '239',
'alignment_length' => '226',
'identity_percentage' => '51.77',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ATR_00003G02210' => array(
'gene_id' => 'ATR_00003G02210',
'e_value' => '4e-66',
'bit_score' => '240',
'alignment_length' => '202',
'identity_percentage' => '56.44',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'WBGene00011631' => array(
'gene_id' => 'WBGene00011631',
'e_value' => '2e-65',
'bit_score' => '234',
'alignment_length' => '227',
'identity_percentage' => '55.95',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'DDB_G0288547' => array(
'gene_id' => 'DDB_G0288547',
'e_value' => '9e-63',
'bit_score' => '220',
'alignment_length' => '212',
'identity_percentage' => '51.89',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'Naga_100003g58' => array(
'gene_id' => 'Naga_100003g58',
'e_value' => '1e-61',
'bit_score' => '221',
'alignment_length' => '203',
'identity_percentage' => '54.19',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AC00G95840' => array(
'gene_id' => 'AC00G95840',
'e_value' => '7e-60',
'bit_score' => '207',
'alignment_length' => '206',
'identity_percentage' => '50.00',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'phs121750' => array(
'gene_id' => 'phs121750',
'e_value' => '2e-58',
'bit_score' => '209',
'alignment_length' => '206',
'identity_percentage' => '50.00',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OS06G08800' => array(
'gene_id' => 'OS06G08800',
'e_value' => '2e-57',
'bit_score' => '204',
'alignment_length' => '206',
'identity_percentage' => '49.51',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ccr132780' => array(
'gene_id' => 'ccr132780',
'e_value' => '2e-56',
'bit_score' => '199',
'alignment_length' => '213',
'identity_percentage' => '48.36',
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'CNC64A_044G00080' => array(
'gene_id' => 'CNC64A_044G00080',
'e_value' => '1e-53',
'bit_score' => '196',
'alignment_length' => '214',
'identity_percentage' => '47.20',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OM_04G01940' => array(
'gene_id' => 'OM_04G01940',
'e_value' => '3e-53',
'bit_score' => '191',
'alignment_length' => '219',
'identity_percentage' => '44.29',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'CV00G61210' => array(
'gene_id' => 'CV00G61210',
'e_value' => '8e-50',
'bit_score' => '179',
'alignment_length' => '211',
'identity_percentage' => '44.08',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'RCC4223.19g00730' => array(
'gene_id' => 'RCC4223.19g00730',
'e_value' => '7e-49',
'bit_score' => '185',
'alignment_length' => '261',
'identity_percentage' => '41.38',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PI00G01490' => array(
'gene_id' => 'PI00G01490',
'e_value' => '2e-48',
'bit_score' => '184',
'alignment_length' => '306',
'identity_percentage' => '37.91',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'gsu74830' => array(
'gene_id' => 'gsu74830',
'e_value' => '9e-48',
'bit_score' => '175',
'alignment_length' => '230',
'identity_percentage' => '42.61',
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'CR06G11280' => array(
'gene_id' => 'CR06G11280',
'e_value' => '1e-46',
'bit_score' => '184',
'alignment_length' => '234',
'identity_percentage' => '42.74',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AP00G00630' => array(
'gene_id' => 'AP00G00630',
'e_value' => '1e-44',
'bit_score' => '175',
'alignment_length' => '242',
'identity_percentage' => '41.74',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'TP02G08210' => array(
'gene_id' => 'TP02G08210',
'e_value' => '3e-42',
'bit_score' => '160',
'alignment_length' => '247',
'identity_percentage' => '38.46',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'BPRRCC1105_14G03340' => array(
'gene_id' => 'BPRRCC1105_14G03340',
'e_value' => '1e-41',
'bit_score' => '156',
'alignment_length' => '183',
'identity_percentage' => '43.17',
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'SPAC2G11.15c' => array(
'gene_id' => 'SPAC2G11.15c',
'e_value' => '2e-41',
'bit_score' => '157',
'alignment_length' => '230',
'identity_percentage' => '39.13',
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'MRCC299_01G06910' => array(
'gene_id' => 'MRCC299_01G06910',
'e_value' => '1e-40',
'bit_score' => '160',
'alignment_length' => '247',
'identity_percentage' => '38.46',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OT_02G01350' => array(
'gene_id' => 'OT_02G01350',
'e_value' => '7e-39',
'bit_score' => '149',
'alignment_length' => '214',
'identity_percentage' => '38.79',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'MP02G06160' => array(
'gene_id' => 'MP02G06160',
'e_value' => '1e-37',
'bit_score' => '149',
'alignment_length' => '254',
'identity_percentage' => '35.43',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PTI_22G00250' => array(
'gene_id' => 'PTI_22G00250',
'e_value' => '4e-34',
'bit_score' => '141',
'alignment_length' => '308',
'identity_percentage' => '32.79',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P064266'
)
),
'CM19G03870' => array(
'gene_id' => 'CM19G03870',
'e_value' => '1e-33',
'bit_score' => '136',
'alignment_length' => '213',
'identity_percentage' => '38.03',
'species' => 'cme',
'common_name' => 'Cyanidioschyzon merolae',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'FC009G01340' => array(
'gene_id' => 'FC009G01340',
'e_value' => '5e-33',
'bit_score' => '134',
'alignment_length' => '229',
'identity_percentage' => '39.30',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AA0018G01160' => array(
'gene_id' => 'AA0018G01160',
'e_value' => '1e-31',
'bit_score' => '124',
'alignment_length' => '102',
'identity_percentage' => '54.90',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'YPL157W' => array(
'gene_id' => 'YPL157W',
'e_value' => '7e-29',
'bit_score' => '123',
'alignment_length' => '181',
'identity_percentage' => '38.67',
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'pte317770' => array(
'gene_id' => 'pte317770',
'e_value' => '1e-28',
'bit_score' => '121',
'alignment_length' => '216',
'identity_percentage' => '32.41',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PTI_22G00920' => array(
'gene_id' => 'PTI_22G00920',
'e_value' => '3e-27',
'bit_score' => '119',
'alignment_length' => '172',
'identity_percentage' => '41.28',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'pte644480' => array(
'gene_id' => 'pte644480',
'e_value' => '1e-25',
'bit_score' => '112',
'alignment_length' => '231',
'identity_percentage' => '32.03',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'pte492450' => array(
'gene_id' => 'pte492450',
'e_value' => '3e-24',
'bit_score' => '108',
'alignment_length' => '231',
'identity_percentage' => '30.74',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'TP07G02910' => array(
'gene_id' => 'TP07G02910',
'e_value' => '8e-22',
'bit_score' => '97.8',
'alignment_length' => '125',
'identity_percentage' => '44.00',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P079127'
)
),
'OL02G04740' => array(
'gene_id' => 'OL02G04740',
'e_value' => '1e-18',
'bit_score' => '87.8',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'FC004G05310' => array(
'gene_id' => 'FC004G05310',
'e_value' => '2e-18',
'bit_score' => '91.3',
'alignment_length' => '180',
'identity_percentage' => '35.00',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P064266'
)
),
'ORCC809_02G02560' => array(
'gene_id' => 'ORCC809_02G02560',
'e_value' => '4e-17',
'bit_score' => '82.8',
'alignment_length' => '79',
'identity_percentage' => '50.63',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'pte690930' => array(
'gene_id' => 'pte690930',
'e_value' => '3e-15',
'bit_score' => '83.2',
'alignment_length' => '196',
'identity_percentage' => '30.61',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P016463',
'ORTHOFAM' => 'ORTHO03P047521'
)
),
'pte615620' => array(
'gene_id' => 'pte615620',
'e_value' => '7e-14',
'bit_score' => '79.0',
'alignment_length' => '201',
'identity_percentage' => '29.85',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P016463',
'ORTHOFAM' => 'ORTHO03P047521'
)
),
'Naga_100031g18' => array(
'gene_id' => 'Naga_100031g18',
'e_value' => '7e-14',
'bit_score' => '77.8',
'alignment_length' => '160',
'identity_percentage' => '29.38',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P028903'
)
),
'phs302960' => array(
'gene_id' => 'phs302960',
'e_value' => '5e-10',
'bit_score' => '67.0',
'alignment_length' => '138',
'identity_percentage' => '32.61',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P028903'
)
),
'ccr191460' => array(
'gene_id' => 'ccr191460',
'e_value' => '3e-07',
'bit_score' => '57.0',
'alignment_length' => '116',
'identity_percentage' => '33.62',
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'gf' => array(
'HOMFAM' => 'HOM03P002616',
'ORTHOFAM' => 'ORTHO03P001814'
)
),
'ES0387G00030' => array(
'gene_id' => 'ES0387G00030',
'e_value' => '1e-06',
'bit_score' => '53.1',
'alignment_length' => '124',
'identity_percentage' => '30.65',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P013338',
'ORTHOFAM' => 'ORTHO03P028903'
)
)
)
$similarity_hits_species = array(
'mus' => array(
(int) 0 => 'ENSMUSG00000093862',
(int) 1 => 'ENSMUSG00000028233'
),
'ppa' => array(
(int) 0 => 'PP00092G00090'
),
'ath' => array(
(int) 0 => 'AT1G45231',
(int) 1 => 'AT1G30550'
),
'emh' => array(
(int) 0 => 'emh729020'
),
'drm' => array(
(int) 0 => 'FBgn0266195'
),
'atr' => array(
(int) 0 => 'ATR_00019G00550',
(int) 1 => 'ATR_00003G02210'
),
'osa' => array(
(int) 0 => 'OS03G27930',
(int) 1 => 'OS06G08800'
),
'esi' => array(
(int) 0 => 'ES0120G00110',
(int) 1 => 'ES0387G00030'
),
'cel' => array(
(int) 0 => 'WBGene00011631'
),
'ddi' => array(
(int) 0 => 'DDB_G0288547'
),
'nga' => array(
(int) 0 => 'Naga_100003g58',
(int) 1 => 'Naga_100031g18'
),
'acg' => array(
(int) 0 => 'AC00G95840'
),
'phs' => array(
(int) 0 => 'phs121750',
(int) 1 => 'phs302960'
),
'ccr' => array(
(int) 0 => 'ccr132780',
(int) 1 => 'ccr191460'
),
'ome' => array(
(int) 0 => 'OM_04G01940'
),
'cvu' => array(
(int) 0 => 'CV00G61210'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.19g00730'
),
'pse3' => array(
(int) 0 => 'PI00G01490'
),
'gsu' => array(
(int) 0 => 'gsu74830'
),
'cre' => array(
(int) 0 => 'CR06G11280'
),
'apr' => array(
(int) 0 => 'AP00G00630'
),
'tps' => array(
(int) 0 => 'TP02G08210',
(int) 1 => 'TP07G02910'
),
'bprrcc1105' => array(
(int) 0 => 'BPRRCC1105_14G03340'
),
'scp' => array(
(int) 0 => 'SPAC2G11.15c'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_01G06910'
),
'ota' => array(
(int) 0 => 'OT_02G01350'
),
'mpu' => array(
(int) 0 => 'MP02G06160'
),
'ptri' => array(
(int) 0 => 'PTI_22G00250',
(int) 1 => 'PTI_22G00920'
),
'cme' => array(
(int) 0 => 'CM19G03870'
),
'fcy' => array(
(int) 0 => 'FC009G01340',
(int) 1 => 'FC004G05310'
),
'aan' => array(
(int) 0 => 'AA0018G01160'
),
'sac' => array(
(int) 0 => 'YPL157W'
),
'pte' => array(
(int) 0 => 'pte317770',
(int) 1 => 'pte644480',
(int) 2 => 'pte492450',
(int) 3 => 'pte690930',
(int) 4 => 'pte615620'
),
'olu' => array(
(int) 0 => 'OL02G04740'
),
'orcc809' => array(
(int) 0 => 'ORCC809_02G02560'
)
)
$gene_id = 'ENSMUSG00000093862'
$all_species_index = array(
(int) 0 => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333'
),
(int) 1 => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702'
),
(int) 2 => array(
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'tax_id' => '763042'
),
(int) 3 => array(
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'tax_id' => '44056'
),
(int) 4 => array(
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'tax_id' => '3075'
),
(int) 5 => array(
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'tax_id' => '41875'
),
(int) 6 => array(
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'tax_id' => '6239'
),
(int) 7 => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055'
),
(int) 8 => array(
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'tax_id' => '310507'
),
(int) 9 => array(
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'tax_id' => '2769'
),
(int) 10 => array(
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'tax_id' => '574566'
),
(int) 11 => array(
'species' => 'cme',
'common_name' => 'Cyanidioschyzon merolae',
'tax_id' => '45157'
),
(int) 12 => array(
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'tax_id' => '44689'
),
(int) 13 => array(
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'tax_id' => '7227'
),
(int) 14 => array(
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'tax_id' => '2880'
),
(int) 15 => array(
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'tax_id' => '280463'
),
(int) 16 => array(
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'tax_id' => '186039'
),
(int) 17 => array(
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'tax_id' => '130081'
),
(int) 18 => array(
'species' => 'hsp',
'common_name' => 'Helicosporidium sp. ',
'tax_id' => '145475'
),
(int) 19 => array(
'species' => 'hom',
'common_name' => 'Homo sapiens',
'tax_id' => '9606'
),
(int) 20 => array(
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'tax_id' => '564608'
),
(int) 21 => array(
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'tax_id' => '296587'
),
(int) 22 => array(
'species' => 'mus',
'common_name' => 'Mus musculus',
'tax_id' => '10090'
),
(int) 23 => array(
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'tax_id' => '72520'
),
(int) 24 => array(
'species' => 'osa',
'common_name' => 'Oryza sativa',
'tax_id' => '4530'
),
(int) 25 => array(
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'tax_id' => '242159'
),
(int) 26 => array(
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'tax_id' => '1486918'
),
(int) 27 => array(
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'tax_id' => '385169'
),
(int) 28 => array(
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'tax_id' => '70448'
),
(int) 29 => array(
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'tax_id' => '5888'
),
(int) 30 => array(
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'tax_id' => '2850'
),
(int) 31 => array(
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'tax_id' => '3218'
),
(int) 32 => array(
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'tax_id' => '67593'
),
(int) 33 => array(
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'tax_id' => '1470871'
),
(int) 34 => array(
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'tax_id' => '249344'
),
(int) 35 => array(
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'tax_id' => '4932'
),
(int) 36 => array(
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'tax_id' => '4896'
),
(int) 37 => array(
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'tax_id' => '35128'
),
(int) 38 => array(
'species' => 'vca',
'common_name' => 'Volvox carteri',
'tax_id' => '3067'
)
)
$all_species = array(
'atr' => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333'
),
'ath' => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702'
),
'acg' => array(
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'tax_id' => '763042'
),
'aan' => array(
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'tax_id' => '44056'
),
'apr' => array(
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'tax_id' => '3075'
),
'bprrcc1105' => array(
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'tax_id' => '41875'
),
'cel' => array(
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'tax_id' => '6239'
),
'cre' => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055'
),
'cnc64a' => array(
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'tax_id' => '310507'
),
'ccr' => array(
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'tax_id' => '2769'
),
'cvu' => array(
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'tax_id' => '574566'
),
'cme' => array(
'species' => 'cme',
'common_name' => 'Cyanidioschyzon merolae',
'tax_id' => '45157'
),
'ddi' => array(
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'tax_id' => '44689'
),
'drm' => array(
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'tax_id' => '7227'
),
'esi' => array(
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'tax_id' => '2880'
),
'emh' => array(
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'tax_id' => '280463'
),
'fcy' => array(
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'tax_id' => '186039'
),
'gsu' => array(
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'tax_id' => '130081'
),
'hsp' => array(
'species' => 'hsp',
'common_name' => 'Helicosporidium sp. ',
'tax_id' => '145475'
),
'hom' => array(
'species' => 'hom',
'common_name' => 'Homo sapiens',
'tax_id' => '9606'
),
'mpu' => array(
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'tax_id' => '564608'
),
'mrcc299' => array(
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'tax_id' => '296587'
),
'mus' => array(
'species' => 'mus',
'common_name' => 'Mus musculus',
'tax_id' => '10090'
),
'nga' => array(
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'tax_id' => '72520'
),
'osa' => array(
'species' => 'osa',
'common_name' => 'Oryza sativa',
'tax_id' => '4530'
),
'olu' => array(
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'tax_id' => '242159'
),
'ome' => array(
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'tax_id' => '1486918'
),
'orcc809' => array(
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'tax_id' => '385169'
),
'ota' => array(
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'tax_id' => '70448'
),
'pte' => array(
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'tax_id' => '5888'
),
'ptri' => array(
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'tax_id' => '2850'
),
'ppa' => array(
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'tax_id' => '3218'
),
'phs' => array(
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'tax_id' => '67593'
),
'pse3' => array(
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'tax_id' => '1470871'
),
'prcc4223' => array(
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'tax_id' => '249344'
),
'sac' => array(
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'tax_id' => '4932'
),
'scp' => array(
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'tax_id' => '4896'
),
'tps' => array(
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'tax_id' => '35128'
),
'vca' => array(
'species' => 'vca',
'common_name' => 'Volvox carteri',
'tax_id' => '3067'
)
)
$gene_family_types_information = array(
'HOMFAM' => array(
'id' => 'HOMFAM',
'name' => 'Homologous gene family',
'prefix' => 'HOM',
'gene_type' => 'coding',
'method' => '{}',
'ancestry' => 'homology',
'parent_id' => ''
),
'ORTHOFAM' => array(
'id' => 'ORTHOFAM',
'name' => 'Orthologous gene family',
'prefix' => 'ORTH',
'gene_type' => 'coding',
'method' => '{}',
'ancestry' => 'orthology',
'parent_id' => 'HOMFAM'
)
)
$gene_family_types_configuration = array()
$data_identifier = 'ENSMUSG00000093862'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'MP06G05470'
$gf_placeholder = 'HOM03P001125'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
'gene_id' => 'CNC64A_044G00080',
'e_value' => '1e-53',
'bit_score' => '196',
'alignment_length' => '214',
'identity_percentage' => '47.20',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
)
$checked = null
$similarity_hit_gene = 'CNC64A_044G00080'
include - APP/View/Analysis/custom_tree_creation.ctp, line 169
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 146
|
1e-53 |
196 |
214 |
47.20 |