How to get unique 1:1 orthologs by Proteinortho?

Question

[haoyan14ioz]

Hi all, I wanna know how to get a 1:1 ortholog using Proteinortho because I got many orthologs had multiple transcripts like below.

# Species   Genes   Alg.-Conn.  trinity_15BJ05.cd-hit.fasta.transdecoder.pep    trinity_60.cd-hit.fasta.transdecoder.pep    
1   3   0.14    Hufu_TR37005|c0_g1_i1|m.38330 Hegu_TRINITY_DN50153_c0_g4_i5|m.67659,Hegu_TRINITY_DN50153_c0_g4_i13|m.67680,Hegu_TRINITY_DN50153_c0_g4_i10|m.67675

1   2   0.248   Hufu_TR100646|c0_g1_i1|m.124281 Hegu_TRINITY_DN37308_c0_g3_i1|m.25758,Hegu_TRINITY_DN37308_c0_g1_i1|m.25757

I have no idea about getting the 1:1 orthologs. Would you like to give me some scripts or some suggestion to do that? I'll really appreciate your help. Thank you.

Answer 1

[natasha.sernova]

Do you insist exactly on Proteinortho?

OMA (Orthologous MAtrix program) has this option and shows n to m, 1 to n, 1:1 orthologs.

http://nar.oxfordjournals.org/content/39/suppl_1/D289.short

This is the mostly citing article about it, they have a lot of new OMA-descriptions.