[Bioperl-l] Blast Output and frac_aligned_query

James Wasmuth james.wasmuth at ed.ac.uk
Tue Jul 20 04:50:55 EDT 2004

Thanks Aaron, time is a slight issue as I'm carrying out several million comparisions but I'll concede accuracy is the more important feature...

For anyone who cares; a quick way to cope with the issue highlighted:
my ($qbeg, $qend) = $hit->range('query');
my $hit_len_q=$qend-$qbeg+1;
my $aln_q_true = $hit_len_q/($res->query_length);


Aaron J. Mackey wrote:

> 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?
> -Aaron
>> 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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