Question: Orthomcl Outputs Just Inparalogs
gravatar for alison.sara.waller
6.2 years ago by
alison.sara.waller0 wrote:

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,


orthomcl • 1.8k views
ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by alison.sara.waller0
gravatar for alison.sara.waller
6.2 years ago by
alison.sara.waller0 wrote:

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 
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
ADD COMMENTlink written 6.2 years ago by alison.sara.waller0


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.

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by tkidder0
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