Question: How to codon a Nucleotide FASTA to Protein FASTA
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gravatar for felix.kuo.1211
3.5 years ago by
felix.kuo.121110 wrote:

I use trinity, and want to use hmmer pfam.

But my trinity file is Nucleotide FASTA.

How can I codon it to Protein FASTA?

rna-seq • 1.4k views
ADD COMMENTlink modified 3.5 years ago by RamRS27k • written 3.5 years ago by felix.kuo.121110

Use transdecoder.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by genomax83k

Another option would be to just run getORF with minimum ORF length on it. You will get more sequences but I -personally- wouldn't use transdecoder, it makes some very funny assumptions in its filtering heuristics, and I have read about very mixed results on Biostars.

Another option would be to run pfam from interproscan which can be run directly on nucleotide data.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Michael Dondrup47k
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