Finding ortholog transcript sequences after de novo transcriptome assembly

Question

[vahapel]

Dear all,

I would like to ask a question about "finding the ortholog transcripts", especially after de novo trancriptome assembly. We have a number of transcript files (assembled with Trinity) and are trying to find ortholog transcript sequences with CDS sequences of eight fish species downloaded from Ensemble ftp (http://www.ensembl.org/info/data/ftp/index.html).

Although there is a good explanation in the Biostar Community (for example; What Is The Best Method To Find Orthologous Genes Of A Species?), most of explanation are relevant with genomic sequences. Can I use (i) Reciprocal Best Hits with Blast, (ii) OrthoMCL or (iii) inparanoid for such a purpose? Or would you suggest me another turnkey solution?

Many thank in advance for all your suggestions,

Answer 1

[mark.ziemann]

Seems the Biostar community has had some trouble with Inparanoid software, so maybe start with OrthooMCL or RBH.

trouble

[vahapel]

Hi Mark,

Thank you for your response and I think that RHB will help me on the topic! New version Inparanoid v8 (http://inparanoid.sbc.su.se/cgi-bin/index.cgi) is also good option.