[Bioperl-l] All-vs-all BLAST

James Wasmuth james.wasmuth at ed.ac.uk
Thu Jul 22 12:42:03 EDT 2004

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


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

Blaxter Nematode Genomics Group  |
School of Biological Sciences    |
Ashworth Laboratories            | tel: +44 131 650 7403
University of Edinburgh          | web: www.nematodes.org
Edinburgh                        |
EH9 3JT                          |
UK                               |	

More information about the Bioperl-l mailing list