[Bioperl-l] Local blast hit (hsp_hseq) extracted from fasta file

Ian Mc Dowell ian.mcdowell at gmail.com
Thu Mar 10 12:13:01 EST 2011


Hi all,

I would like to take local blast hit sequences, i.e. hsp_hseq in blast xml
format, and extract the full sequences of those hits from the original fasta
file and put them in a fasta file of all hits that I can use later.

This should be a widely performed task but I can't find any scripts that
directly address this issue.  I have not acquired the skills to make my own
scripts for this task.

Thanks so much if you have anything that can help me out,

Ian McDowell
Aquatic Pathology
University of Rhode Island


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