[Biodevelopers] Re: BLAST asymmetrical

[Christopher Dwan]

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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