[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
>> 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
>> 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
More information about the Bioperl-l