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; https://www.biostars.org/p/7568/) , 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,