Strand aware gff3 to protein fasta

Question

[karthic]

Hi everyone,

I know there are lots of program which can translate the nucleotide fasta to protein fasta in all 6 frames or the frame we desire. But is there any program which can take genome fasta + gff3 table and give protein fasta as output by taking the strand of each sequence also into consideration??

Thanks, Karthic

[lieven.sterck]

What exactly do you mean?

translating the CDS present in the GFF3 file into a correct protein (correct reading frame, strand , ... )? If so, there should be plenty tools that does this (== it is/should be the default normally).

A few tool examples that come to mind: AGAT, getFasta from bedtools, ...

[karthic]

Thanks for your reply. I have used bedtools fasta, I can force strandedness but it outputs only as nucleotide fasta. Not sure about AGAT, going to install. But from the list of program names, I am unable to find the requisite one.

[lieven.sterck]

I see, if you're able to get to the nucleotide sequence you can run those through eg EMBOSS transeq to get to the protein (AA ) sequence.

Though I can't directly point you to the suitable AGAT subprogram, I would be very surprised if it can't do this.