RSAT - get-orthologs manual

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 :