[Bioperl-l] HSP tiling problem

=?gb2312?B?va3OxOL9?= biology0046 at hotmail.com
Mon Sep 15 16:00:02 EDT 2008


Dear all:
I try to use bioperl's SearhIO module to parse the blast output, 
the output of blast contain many HSPs from the same hit, each HSP come out with an count of identity residues and alignment length, but what i want to get is the global identiy and alignment length of the query sequence and hit sequence, which may be done by tiling the HSPs and build a HSP contig, 
 
the bioperl BLASTutil module contain "hsp_tiling and length_aln, frac_identical" method fullfill my purpose, but i read through the mailing list, some user said the method used by bioperl were not precise in many cases, they sugguest to use WUBLAST.
 
but i don't know which WUBLAST opinion should i use, i use "links" opinion, but the output still give me lots of HSPs, are these HSPs created from some small HSPs?best regards!wenkaichinese academy of sciences
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