Orthomcl Pairs

Question

[jollymrt]

hi all, i am getting a populated InParalog table but empty ortholog and coortholog tables, i have set the % match to 20% but still the tables are empty.Any ideas?

[Niek De Klein]

Can you give more detail of what you are doing using what technologies/software and what exactly goes wrong?

[jollymrt]

I am using orthoMCL 2.0.3 to identify orthologs for a small set of proteins.the problem is I am getting populated InParalog table but nothing goes in the ortholog table.

Answer 1

[Torst]

OrthoMCL will only find orthologs if you give it separate files for each organism. If you put them all in one file it thinks they are all from the same organism, and hence calls them paralogs instead.

eg. orthomcl.pl --mode 1 --fa_files Species1.faa,Species2.faa