[Bioperl-l] Blast Output and frac_aligned_query

Aaron J. Mackey amackey at pcbi.upenn.edu
Mon Jul 19 10:07:35 EDT 2004

BLAST is a great search algorithm, but a pretty poor pairwise alignment 
algorithm (i.e. bl2seq).  Why not use Smith-Waterman (and/or LALIGN, if 
you're interested in repeats) if you want to get a "believable" 
alignment with which to do further analysis?

HSP tiling is a process for stringing together incomplete alignments; 
no matter how you do it, you're never guaranteed to get the "right" 
answer.  So why worry about doing it better, when you shouldn't be 
doing it at all?


> On Mon, 19 Jul 2004, James Wasmuth wrote:
>> First apologies if this has been debated before, didn;t see it in the
>> archive and been away for a while, so unlcear on current state of 
>> affairs.
>> I have a bl2seq output (below) and when I extract its statistics, I am
>> told that 156% of the query is aligned.
>> This is probably because of multiple HSP produced as the protein 
>> appears
>> highly repetitive. Would this mess up the tiling the hsps, in its
>> current implementation?

Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  amackey at pcbi.upenn.edu
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697

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