DESCRIPTION

Given a gene or a list of genes from a query organism, and a reference taxon, this programs returns the orthologs of the query gene(s) in all the organisms belonging to the reference taxon.

AUTHORS

Rekin’s Janky

Jacques.van-Helden\@univ-amu.fr

INPUT FORMAT

Query genes can be directly entered on the query input or in an input file.

The first word of each row of input file is considered as a query. Any additional information on the same row is ignored.

OUTPUT FORMAT

A tab-separated file with two (or more) columns. Each row of the output file describes one similarity between a query gene and another gene (ortholog or paralog, depending on the parameters).

RETURN FIELDS

The program returns at least these three first columns :

1. ref_id the first column indicates the "hit" gene (the target one identified by BLAST as similar to the query)


2. ref_org the second column gives the reference organism (the target organism in which the BLAST search was performed).


3. query the third column indicates the ID of the query gene.

Additional columns can be specified :

• ref_name
  Name of the reference gene.
  
  
• query_name
  Name of the query gene.
  
  
• query_organism
  Name of the query organism.
  
  
• ident
  Percent of identity (a number between 0 and 100)
  
  
• ali_len
  Alignment lengths (in residues).
  
  
• mismat
  Number of mismatches.
  
  
• gap_open
  Number of gap openings.
  
  
• E-value
  E-value (expected number of false positives).
  
  
• bit_sc
  Bit score.
  
  
• rank
  Rank of this query gene among all those matching the same reference (target) gene for this pair of organisms.
  
  
• reciprocal rank
  Rank of the hit in the reciprocal BLAST.

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  ORTHOLOGY CRITERIA

  Actually, this program allows to retrieve orthologs, but also paralogs.

  The detection of pairwise similarities is based on a bidirectional BLAST of each genome against each other. During the detection phase, multiple hits for a single gene are allowed, and the user can decide to filter them out or not.

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  REFERENCES

  Janky R, van Helden J. Discovery of conserved motifs in promoters of orthologous genes in prokaryotes. Methods Mol Biol. 2007;395:293-308.