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12-01-2013, 10:24 PM
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#1 |
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Junior Member
Location: New Delhi Join Date: Sep 2011
Posts: 5
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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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12-11-2013, 01:11 AM
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#2 |
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Senior Member
Location: Denmark Join Date: Apr 2009
Posts: 153
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Have a look at get_seq from Biopieces (www.biopieces.org):
https://code.google.com/p/biopieces/wiki/get_seq |
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