Introductionary tutorial

This tutorial contains the necessary standard information for new users to get started. A more detailed overview (with indicative figures) of the crucial web pages in PLAZA can be found here.

Finding the correct tools for the job is important. The following table gives an indication of what tools are available in PLAZA, and how you can get to the point of using them. A detailed overview for each tool can be found here.

Tool Usage How to get there
AnnoJ Genome browser Organism page→View organism in genome browser.
or Gene page→Toolbox→View the gene in the Genome Browser.
BLAST BLAST interface Menubar→Analyze→BLAST
Circle Plot Genome evolution / Colinearity research Menubar→Analyze→WGDotplot
Conversion tool Gene identifier conversion Menubar→Archive→Conversion tool
Expansion Plot Gene family expansion plot Menubar→Analyze→Expansion plot
Functional Clustering Functional clustering gene annotations Menubar→Analyze→Functional clusters
Gene Family Finder Find expanded or enriched gene families Menubar→Analyze→Gene Family Finder
or Species/Clade page→Toolbox→View specific or enriched gene families
Genomeview Genome browser Organism page→View organism in genome browser.
or Gene page→Toolbox→View the gene in the Genome Browser
Integrative Orthology Viewer Overview orthologous genes Gene page→Toolbox→Explore the orthologous genes in other species.
or Workbench experiment overview→Toolbox→View the orthologous genes
Jalview Gene family evolution / Explore multiple sequence alignment Gene family page→Toolbox→View the multiple sequence alignment
or Gene page→Toolbox→Explore the multiple sequence alignment of the homologous gene family
Ks-dating Tool Genome evolution / Colinearity research Menubar→Analyze→Ks-dating tool
Multiplicon View Genome evolution / Colinearity research From chromosome view in WGDotplot, click on a colinear region
Similarity heatmap Gene family evolution / Explore gene similarity Gene family page→Toolbox→View the similarity heatmap
Skyline Plot Genome evolution / Colinearity research Menubar→Analyze→Skyline plot
or Gene page→Toolbox→Explore the colinearity of this gene with other genomes
Synteny Plot Genome evolution / Colinearity research Menubar→Analyze→Synteny plot
or Gene page→Toolbox→Explore the local gene organization for homologous genes.
or Gene family page→Toolbox→Explore the local gene organization for homologous genes
Tree Explorer Gene family evolution / Phylogenetic tree representation Gene family page→Toolbox→Explore the phylogenetic trees
or Gene page→Toolbox→Explore the phylogenetic tree of the homologous gene family
WGDotplot Genome evolution / Colinearity research Menubar→Analyze→WGDotplot
or Gene page→Block Duplicate1
WGMapping Mapping of gene sets on chromosomes Menubar→Analyze→WGMapping
or Gene family page→Toolbox→View the genome wide organization of this gene family
or Workbench experiment overview→Toolbox→View the genome-wide organization
Workbench Analyze custom gene set Menubar→Analyze→Workbench

1Only available for genes with paralogs in a duplicated region (block duplicates)

There are several options provided in PLAZA to find genes or gene families you're interested in.

On every page (except for the DokuWiki pages) there is a box that allows users to quickly find the genes they are interested in, the Search bar. The different search options are listed below, together with a sample term that can be used each time:

  • Gene description : This is the most general search. It will look for all genes with a certain term in their description. Unfortunately only very well annotated genomes have these descriptions, so it will usually return Arabidopsis and Rice genes. However, the view Associated gene families link provides a elegant alternative to circumvent this problem (see below). This search function is also very useful to find genes using their common name (eg. Alcohol dehydrogenase, PIN1,…) Please note that wildcards are added automatically, using ADH as a term will return NADH, ADH1,ADH2, … as well.
  • GO/InterPro description : Selecting this option will first find all GO term and InterPro domains with a certain description and then fetch all the genes associated with these labels. Parent-child relations of GO terms are taken into consideration and therefore will give all relevant genes (even those with a more detailed GO term associated. (eg. Golgi apparatus part finds proteins with COPII as a label, for more information see functional annotation)
  • Gene : Use this option to find genes based on their PLAZA gene id. Note that these are in some cases (Arabidopsis, Rice & Sorghum) the same as used by TAIR, TIGR and JGI. We always use ID in the following format: PT02G01010 the PT is a two letter code indicating the species (here a Populus trichocarpa gene is used), the 02 indicates the chromosome and the last number is the id based on the position (this can be 6 or 7 digits; eg. AT2G17380). Note that also the original gene ID assigned by the primary data provider (eg. Populus JGI gene name grail3.0066015301) can be used in this search function.
  • Gene family : Find a gene family or sub-family based on it's PLAZA id. (format: HOM + 6 digits for families and ORTHO + 6 digits for sub-families eg. HOM000400)
  • GO term : To retrieve information about a gene ontology term select this option (eg. GO:0009926)

Apart from searching individual genes, most result pages also provide a link Associated gene families that will project all returned genes to their corresponding gene families (see the tutorial on functional annotation). This provides an intuitive and fast approach to study gene family distributions in different species (starting from a gene description, GO term or InterPro search).

BLAST

In case you're unable to find the gene using the keyword search function, or the gene is from a species not included in PLAZA and you are looking for similar genes (with the protein sequence or DNA coding sequence), you can use the BLAST search (found in the menu Analyze→BLAST). You need to copy&paste your sequence in FASTA format and set the database you'd like to BLAST against (plaza_proteins or plaza_transcripts) and select the appropriate BLAST algorithm.

  1. BLASTN compares a nucleotide query sequence against a nucleotide sequence dataset
  2. BLASTP compares an amino acid query sequence against a protein sequence dataset
  3. BLASTX compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence dataset
  4. TBLASTX compares the six-frame translations of a DNA sequence to the six-frame translations of a nucleotide sequence dataset.
  5. TBLASTN compares a protein query sequence against a nucleotide sequence dataset dynamically translated in all six reading frames (both strands)

For genes present in PLAZA you can use the Toolbox option View BLAST hits against the PLAZA database. this will get the BLAST results instantly from our database (precomputed). In case you would like to run the BLAST again using different parameters, additional buttons are provided to guide you to the BLAST page.

A full description of the BLAST web interface can be found on the Bioinformatics website.