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Old 12-01-2013, 10:24 PM   #1
Junior Member
Location: New Delhi

Join Date: Sep 2011
Posts: 5
Default flanking sequences extraction

I have a file containing identifiers and their mapping positions.

first file looks like
contig0003 526 956
contig0009 685 985

second file contains fasta sequences , containing these identifiers. Now i want to extract flanking sequences on both sides. i.e start from -100 to 250, containing the original sequence. Can anybody please provide me with any perl script or any other command.
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Old 12-11-2013, 01:11 AM   #2
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Location: Denmark

Join Date: Apr 2009
Posts: 153

Have a look at get_seq from Biopieces (
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