Conversion of fna files to faa
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6 weeks ago
Sharon ▴ 10

Hi, Can someone tell me how I can convert multiple fna files of bacterial genomes to faa files using the command line? I have downloaded these files from NCBI. I have looked up the sed code but was unable to use it properly.

NCBI command Bacteria line • 241 views
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6 weeks ago
Mensur Dlakic ★ 15k

There is no simple conversion for what you want. By most commonly accepted nomenclature, the .fna files contain genomic sequence(s), while the .faa files contain proteins that are predicted from the genomic DNA. It is not a matter of conversion - one needs to predict the genes. My advice to you is to download the .faa files from the same site where you got the .fna files. If they are not available, prokaryotic genes can be predicted using prodigal. While you should read about all the program options, a typical command to get what you want would look something like this

prodigal -i file.fna -a file.faa -o /dev/null

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That helped clear things a lot. Thank you very much