[Bioperl-l] using LargeSeq objects

Michael R Olson olsonmr at stolaf.edu
Mon Jun 23 15:49:32 EDT 2003

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);

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.

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