[Bioclusters] Blast Source

[Tim Harsch]

Wow!  Thank you all so much for the quick and informative replies.  It gives
my colleague and I some stuff to dig into.

...  I've always liked this list, the people here are knowledgable and eager
to help.

Thanks again.
Ciao,

----- Original Message -----
From: "Chris Dwan (CCGB)" <cdwan@mail.ahc.umn.edu>
To: <bioclusters@bioinformatics.org>
Sent: Tuesday, April 15, 2003 4:47 PM
Subject: Re: [Bioclusters] Blast Source


>
> Depending on the exact goals of your analysis, BLAST can be a poor choice
> for finding matches with very low sequence identity.  It was designed as,
> and remains, an excellent, fast approximation to exhaustive pairwise
> search (a la Smith & Waterman).
>
> If you managed to turn the word size all the way down to 1 (or 2), you
> would have complete sensitivity.  Effectively, this would disable the
> heuristic by which BLAST achieves its speedup.  Another parameter to play
> with is "neighborhood word size."  This parameter defines the distance (in
> alignment score) of neighbors which BLAST will also allow as "perfect
> matches" in the hit generation phase.
>
> Really though, if you're searching for interestingly distant pairs,
> another methodology might be in order.  If the sequences in question share
> only 25% identity, it's unlikely that you're going to find them above the
> noise, even if you manage to turn the "sensitivity" knob on BLAST all the
> way up.
>
> Statistical methods like motifs, PSSMs, PSI-BLAST, and HMMER have all been
> used to greatly increase the sensitivity of such searches over pairwise
> techniques.  Beyond these are structurally based methods, which are
> popping up all over the place these days, as we finally have enough good
> structure data to construct meaningful patterns.
>
> Good luck.
>
> -Chris Dwan
>  Center for Computational Genomics and Bioinformatics
>  University of Minnesota
>
> > A colleague of mine is trying to use blast to determine very loose
matches.
> > He would like to change the minimum seed length, which is hard-coded
into
> > Blast, from 7 to 5.  Does anyone know a backdoor way, ie undocumented
> > parameter, which could do this?  Or, where we might find the blast
source
> > code so we can make this change manually?
>
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