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********************************************************************************
*******                                                                  *******
*******    Ectocarpus siliculosus file download                          *******
*******                                                                  *******
********************************************************************************

This readme file contains general information and descriptions of the files
available for download.

All files are zipped with gzip to reduce the size and thus decrease download
time. To unzip a gzip file use 'gunzip' on unix, on windows systems use a program
like 7-zip (freeware). Some of the downloadable files are actually tar archives 
that contain several files (sometimes quite a lot), this is typically for embl and 
gff files.

The most up-to-date version of the data files is always called _LATEST.
No record is being kept of these files so when updates are available, the
present files will be overwritten by the new ones.

Embl files only contain information on the features present on a genomic 
scaffold (=> feature tables), they do not contain the sequence itself.


=================================================================================
Files and Directories:
=================================================================================
Ectsi_cds_LATEST.tfa.gz        CDS of the most recent version of the gene models
Ectsi_prot_LATEST.tfa.gz       Proteins of the most recent version of the gene models
Ectsi_mRNA_LATEST.tfa.gz       mRNA sequences of the most recent annotation. mRNA = 
                               CDS + UTR (UTR is only assigned based on EST evidence).
Ectsi_embl_LATEST.tar.gz       Embl-formatted file of the genome annotation
Ectsi_gff_LATEST.tar.gz        GFF formatted file of the genome annotation
Ectsi_gff3_LATEST.tar.gz       GFF3 formatted file of the genome annotation
Ectsi_gene_info_LATEST.txt.gz  tab delineated file with basic info on each gene
                               (start,stop, GO-labels, functional description, protein 
										 domains)
Ectsi_genome_V2_cleaned.tfa.gz Fasta file of all the scaffolds in the genome assembly file
Ectsi_genome_InfEg2kb.fasta.gz Fasta file with all the contigs smaller than 2Kb. (not part
                               of the main assembly)
Ectsi_intergenic_cds.tfa.gz    Fasta file containing upstream intergenic sequence (1Kb)
                               counted from the start of the CDS
Ectsi_intergenic_utr.tfa.gz    Same as above but taking UTR into account, 1Kb upstream of
                               start of UTR (if present, otherwise start of CDS)						  
Ectsi_mask.tar.gz              The output from RepeatMasker denoting the masked regions
                               in the genomic sequences. (tab-delineated file)
Ectsi_TE_Lib.tfa.gz            The transposons library used to mask the genome, in fasta format

Archive/                       Directory containing older verions of the annotation
Ectsi_*_Jun2010.* files        These files contain the version of Jun2010 (=older version)
Ectsi_*_Oct2010.* files        These files contain the version of Oct2010 (=older version)
 
=================================================================================
File formats:
=================================================================================
Ectsi_gene_info_LATEST.txt.gz  tab-delineated file format,
                               columns: <contig> <gene name> <start> <stop> <definition-line> <GO> <domains>

=================================================================================
Last Modified on: May, 2th, 2011
contact: beg-bogas[at]psb.vib-ugent.be