How to codon a Nucleotide FASTA to Protein FASTA

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

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updated 9.7 years ago by Ram

• written 9.7 years ago by felix.kuo.1211 •

Use transdecoder.

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written 9.7 years ago by GenoMax

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.

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written 9.7 years ago by Michael Dondrup

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