Command line tool for translated multifasta nucleotide to aminoacid sequence

Question

[dllopezr]

Hi everybody

I have several multifasta files with nucleotide gene sequences. Could you give me recommendations of command line tools to translated this files to aminoacid sequences in new files with the same title and headers of origin?

Thank you!!

Answer 1

[cpad0112]

faTrans from kentutils.

[GenoMax]

Added a link for linux executable. You will need to do chmod a+x faTrans after download before you start using it.

[cpad0112]

Thanks @genomax

Answer 2

[GenoMax]

You can use EMBOSS transeq. Not sure if it will write the headers through as is.

[firestar]

It keeps the fasta headers but seems to do some cleaning. In my case, commas (,) were converted to underscores (_). Turns out this can be turned off using -sformat pearson (https://www.biostars.org/p/111857/).