[Bioperl-l] Blast Output and frac_aligned_query
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 $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?
>> 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
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
I like nonsense, it wakes up the brain cells.
-- Dr. Seuss
Blaxter Nematode Genomics Group |
School of Biological Sciences |
Ashworth Laboratories | tel: +44 131 650 7403
University of Edinburgh | web: www.nematodes.org
EH9 3JT |
More information about the Bioperl-l