Ways to convert fasta to faa file for functional annotation?

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4.7 years ago

c.e.chong ▴ 60

Hi All,

I want to convert a multifasta file (containing the nucleotide sequences of genes from the pangenome.fa output from Roary) to an amino acid sequence file, so I can input it into eggNOG-mapper to functionally annotate COGs.

Does anyone know a good way to do this?

Thank you in advance!

pangenome Roary Assembly annotation • 2.3k views

ADD COMMENT • link updated 4.6 years ago by Biostar 20 • written 4.7 years ago by c.e.chong ▴ 60

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Is there a reason you want to convert? I think eggNOG mapper takes CDS sequences also as input.

ADD REPLY • link 4.7 years ago by gayachit ▴ 200

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I didn't see this option!! Thank you.

ADD REPLY • link 4.7 years ago by c.e.chong ▴ 60

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You just need to translate the sequences with the relevant codon table for your organism. This is quite common and there are lots of tools that can do this.

A better solution though, which will be more accurate and true to the original data, would be to take the IDs of the genes you have, and then use those ID's to pull out the corresponding protein sequences from the original genbanks. You will need to show us your data for us to be much more help however.

ADD REPLY • link 4.7 years ago by Joe 21k

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