Extract doimain sequence from interproscan gff file result

Question

[roelr]

I have a gff file from interproscan output that I want to extract the conserved domain that was identified from the results. Is there a way to do this without having to do it manually? My data are bZIP TF that I run in interproscan to identify domains in the seq data. I just want to extract the bZIP domain from the result.

Answer 1

[h.mon]

Probably you can use bedtools getfasta:

1) subset your gff to contain only domains of interest;

2) bedtools getfasta -fi sequences.fasta -bed bzif.gff