[Bioperl-l] using LargeSeq objects
morten at binf.ku.dk
Mon Jun 23 18:05:06 EDT 2003
Michael R Olson wrote:
>I'm currently writing a program that runs BLAST, then gets the start and
>stop base pairs of the alignment for a hit and goes to the database
>BLAST was run against, and gets base pairs before and after the start
>and stop. Right now I use LargeSeq objects to read the entire database
>into memory (or a chunk, if it's divided up) and then say
>$str = $seq->subseq($start,$end);
Remember that the exact start and stop depends on the parameter setting
for blast - falloff etc.
>Is this significantly less efficient than going into the database myself
>and using seek, tell and read, because using SeqIO objects is much
>easier, but right now it's very slow.
Use Bio::DB::Fasta - it is very fast and just as convenient.
Go: perldoc Bio::DB::Fasta. I haven't been able to locate the
documentation on the website.
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