[Bioperl-l] extracting subsequences

Amit Indap indapa at gmail.com
Tue Oct 25 16:48:09 EDT 2005


I have to extract subsequences from fasta files containing entire
human chromosomes. For example I would like to extract bp
167506667..167523040. I know how to do this using the Bio::Seq and
Bio::SeqIO APIs. The problem is it takes a long time to read in an
entire fasta file containing a chromosome. Is there a way I can speed
this up?

The bp indices are taken from BLAT-ing my sequences to the genome. I
could use megablast to find which contigs my sequences lie on, and
then read in those files rather than the whole chromosome.

Any suggestions would be helpful. Thanks.

Amit Indap

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