Question: Finding ortholog transcript sequences after de novo transcriptome assembly
0
gravatar for vahapel
4.9 years ago by
vahapel170
Turkey
vahapel170 wrote:

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; 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,

blast rna-seq alignment gene • 1.7k views
ADD COMMENTlink modified 4.9 years ago by mark.ziemann1.2k • written 4.9 years ago by vahapel170
0
gravatar for mark.ziemann
4.9 years ago by
mark.ziemann1.2k
Australia/Mebourne/Geelong/Deakin
mark.ziemann1.2k wrote:

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

Anybody Managed To Make Inparanoid Work? 

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by mark.ziemann1.2k

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.

ADD REPLYlink written 4.9 years ago by vahapel170
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