[Bioperl-l] How to obtain Up- and Downstream target-Sequences of Blast Matches

jobu buschj at hhu.de
Sun Jul 15 15:46:42 EDT 2012


Dear All.

Still being a beginner in Perl and just having started to look into
BioPerl, I hope to ask my question at the right place.

I locally ran a standalone blastn search of many short query-sequences
against a set of target-fasta-sequences consisting of whole chromosomal
sequence data.

What I need to do now is to get let's say 100nt each Up- and Downstream
out of my target sequences for each Blast match.

At this point I only can assume that BioPerl might be helpfull in
resolving this task, though I haven't found a module yet that will
manage to do this locally on my harddrive.

Thus I would be thankful for the slightest hint where to begin.

Sincerely
Jochen


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