Orthomcl Outputs Just Inparalogs

Question

[alison.sw]

Dear all,

I would like to determine orthologs (specifically also paralogs and coorthologs) between 2 bacterial species (EColi MG1655 and Salmonella 14028S).

I tried using orthoMCL I followed all of the 13 steps however, after my orthomclPairs command, all of the pairs are in the inparalogs.txt file.

Has anyone else had a similar error?

Any help appreciated,

thanks

Answer 1

[alison.sw]

I think there must be a problem in generating the similarSequences file. Looking at this output it looks like it thinks that all of the proteins are from sa14.

has anyone had problems creating this similar sequences file?

$ head similarSequences.eco.sa14.try1 
eco|NC_000913.2_cdsid_NP_414543.1    eco|NC_000913.2_cdsid_NP_414543.1    sa14    sa14    0    0    100    100
eco|NC_000913.2_cdsid_NP_414543.1    sa14|NC_016856.1_cdsid_YP_005235635.1    sa14    sa14    0    0    94.5    100
eco|NC_000913.2_cdsid_NP_414543.1    eco|NC_000913.2_cdsid_NP_418375.1    sa14    sa14    8    -92    30.7    97.5
eco|NC_000913.2_cdsid_NP_414543.1    sa14|NC_016856.1_cdsid_YP_005240382.1    sa14    sa14    6    -90    30.8    97.5

[tkidder]

Hello,

I am having exactly the same problem, and I know this is a long shot, but is there any chance you found the solution?

EDIT: Found a solution: A: Orthomcl Pairs
I was running a file 'all.fasta' that consisted of concatenated fasta files as opposed to using individual fasta files.

Answer 2

[pooja.singh09]

Hi

I have the same issue, orthologs.txt and coorthologs.txt files are empty after using orthomcldumppairs command. I am using separate fasta files for the 2 species. Weirdly, it all works fine for my one dataset but not for the other! Cannot figure out the issue.