[Bioperl-l] extracting subsequences

[Amit Indap]

Hi,

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
--
Amit Indap
http://www.bscb.cornell.edu/Homepages/Amit_Indap/