[Inparanoid] Inparanoid 4.1 standalone output
Steffen Priebe
steffen.priebe at hki-jena.de
Wed Feb 11 13:37:30 CET 2015
I applied the inparanoid standalone version 4.1 to find homologs between
two species
using 2 protein FASTA files. Inparanoid generated the following output
files:
orthologs.species1.fasta-species2.fasta.html
Output.species1.fasta-species2.fasta
table.species1.fasta-species2.fasta
sql.species1.fasta-species2.fasta
species1.fasta-species2.fasta
species1.fasta-species1.fasta
species2.fasta-species2.fasta
The HTML file and the Output.* file both list the number of orthologe
groups found,
as well as the number of in-paralogs in each species:
9888 groups of orthologs
12352 in-paralogs from species1.fasta
11012 in-paralogs from species2.fasta
Anyhow, the Output.* file additionally outputs the following numbers (in
the first 4 lines):
23603 sequences in file species1.fasta
20208 sequences in file species2.fasta
20845 sequences species1.fasta have homologs in dataset species2.fasta
17870 sequences species2.fasta have homologs in dataset species1.fasta
I was wondering where to find these genes listed in line 3+4, which are
larger compared to the number of in-paralogs?
In the 4 output files (orthology.*.html, Output.*, table.*, sql.*) only
the 9888 groups including the 12352 and 11012 genes are listed.
It also not clear to me how to output in the last 3 files is organised
and what each column means:
Example of the first 3 rows:
gene1.species1 gene1.species2 184.1 110 541 92 92
92 92 q:1-92 h:439-530
gene1.species1 gene2.species2 181.0 110 539 97 97
97 97 q:1-97 h:440-536
gene1.species1 gene3.species2 50.1 110 211 81 82 81
82 q:1-81 h:123-204
..
There was no description for these kind of output.
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