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Extract doimain sequence from interproscan gff file result

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.

conserved domain
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updated by h.mon h.mon • written by roelr • roelr

1 answer

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

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written by h.mon h.mon

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