Sequences number of Orthomcl results (groups.txt) were lower than raw data (fasta file)

Question

[Ginsea Chen]

Hello everyone!

I tried to cluster 10000 protein sequences through Orthomcl, while my Orthomcl results (groups.txt, the output file of orthomclMclToGroups) only contained 6853 sequences. Is it suitable? I thought the mismatch may be for unsuitable blast tool were used, so I want to know which blast tool commonly used in orthomcl analyses, blast2 or blast+?

Thanks

Answer 1

[DG]

I'm not 100% sure but I believe that OrthoMCL doesn't output singletons at the pairs and groups stage of the analysis. I would suspect that that is what makes up the bulk of your missing values. You could check this by looking at the BLAST results for sequences that didn't make it to the output stage and see what their BLAST scores/hits look like.