How to get unique 1:1 orthologs by Proteinortho?
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.
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natasha.sernova
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haoyan14ioz •
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haoyan14ioz •
1 answer
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.
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