[Bioperl-l] All-vs-all BLAST

[James Wasmuth]

If the idea is to look for "domains" two recent studys both with 
excellent reviews in their introductions are:

Bioinformatics - 20:1335 (2004)
NAR - 32:3522 (2004).

I can't remember how this thread started, but I'm sure the phrase "no 
point in re-inventing the wheel" was used, and there really isn't with 
regard to "domain" prediction unless you are hell-bent on it.

Anyway that's my £0.02 ($0.036) worth

-james



Josh Lauricha wrote:

>On Thu 07/22/04 11:32, Andreas Kahari wrote:
>  
>
>>On Thu, Jul 22, 2004 at 11:09:45AM +0100, Peter van Heusden wrote:
>>Or MCL, which I think Jason has provided some blast-related
>>input to:
>>
>>    http://micans.org/mcl/
>>    
>>
>
>In my experiance MCL gave fairly horrible results when used with
>proteins that may have "fused" domains. But then, all the ones we tried
>were flawed. MCL just claimed to deal with multiple domains. Anyhow,
>this was last summer so a) it might have changed or b) I'm remembering
>another program, even c) I'm just plain wrong ;)
>
>Even so, I think MCL still requires an All vs All blast.
>
>Another option (which is installed with blast) is blastclust. This
>does single linkage, so it's not that great if you have multiple
>domains in your proteins, but none are. The problem is, with
>multiple domains you end up clustering like:
>----------- --------------------- --------------
>------
>------
>-------
>--------
>             ------------
>             --------------
>              -----------------
>            ---------------
>                                        ---------
>                                     --------
>                                        ---------
>
>where that should be three clusters, it gets grouped into one.
>
>Can stackPACK(?) deal with that gracefully?
>
>  
>

-- 
I like nonsense, it wakes up the brain cells.
		-- Dr. Seuss

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