[Biodevelopers] Re: BLAST asymmetrical

[Martin Gollery]

My apologies, Chris, I see what you are saying and you are correct-
S/W is not a good program for genome/genome comparisons because it
does not show all the sub-optimal alignments. Somebody modified it so
that it would do this, but I can't recall the name.

Double-affine S/W will do much better at this sort of thing, but it
fails to catch rearrangements- this is not what it is designed for.
Double-affine S/W would be ok if the genomes are close, but not
otherwise.

Marty

On 1/22/07, Christopher Dwan <cdwan at bioteam.net> wrote:
>
> You are correct, I misspoke.  S/W is a local alignment algorithm.  It
> provides, in its raw form, the best set of local alignments between
> the two chromosome sequences.   Sorry for any confusion that may have
> caused.
>
> Unless I'm seriously mistaken, the point remains:  S/W will take a
> really long time and its results will be (in raw form) of limited
> biological value.  It certainly won't return "all homologies," or
> really anything close to them.
>
> -Chris Dwan
>
> It'll still, in its raw form,
>
> On Jan 21, 2007, at 1:59 AM, Martin Gollery wrote:
>
> > Smith/Waterman is not global, Chris- it's local. It's Needleman-Wunsch
> > that is global.
> >
> > On 1/20/07, Christopher Dwan <cdwan at bioteam.net> wrote:
> >>
> >> > I want all homologies.
> >> >
> >> >> Or even Smith-Waterman which will take a while to run.
> >> >
> >> > Do you know of a program that can calculate SW on a pair of
> >> genomes?
> >>
> >> This may be a semantic confusion on my part, but here's my answer to
> >> that specific question:
> >>
> >> If you really want the single best *global* alignment between two
> >> multi megabase sequences, yes SW is the way to go, and yes, it will
> >> take a really long time.  On the other hand, I've never met anyone
> >> who really, seriously cares about monolithic, global alignments of
> >> chromosomes.  Go down that road, and the next question will be "why
> >> can't we just run clustalw on whole chromosomes?"  Yes, of course you
> >> could ... but it'll be really slow and not very useful.
> >>
> >> Note:  This is not an invitation to the accelerator people in the
> >> audience to offer me a *faster* clustalw or SW.  I'm trying to steer
> >> people toward *better* uses of the tools.  You might as well work on
> >> multi-gigabyte cut-and-paste buffers so that I can stuff whole
> >> genomes into the NCBI web interface.
> >>
> >> On the other hand, if you want the best gene sized (a few kilobase)
> >> matches from within that pair of megabase sequences, it's a different
> >> question.  You're going to wind up chopping each sequence into
> >> overlapping chunks and running an all against all search of some
> >> sort.  The chunk size will be determined by how large you think the
> >> introns and exons in your genes are.  An even more clever approach
> >> might involve doing preliminary gene calls with a gene finding
> >> program like Glimmer, and then starting the all against all search
> >> from those hits.
> >>
> >> Chromosome vs. chromosome BLAST answers the question "is there a
> >> decent hit to any part of this chromosome in that other one".  The
> >> answer, broadly speaking, will be "yes, there is a statistically
> >> significant match there."
> >>
> >> If you want homologous genes, you're going to have to do a bit more
> >> work than just running a single program to get The Answers.
> >>
> >> -Chris Dwan
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> >>
> >
> >
> > --
> > --
> > Martin Gollery
> > Associate Director
> > Center For Bioinformatics
> > University of Nevada at Reno
> > Dept. of Biochemistry / MS334
> > 775-784-7042
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-- 
-- 
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS334
775-784-7042
-----------