[BioPython] Eliminating redundancy : how?
Ramu Chenna
chenna@embl-heidelberg.de
Thu, 12 Jul 2001 10:04:29 +0200
Hi
Why do not you use nrdb (ncbi one ) or
nrdb90
Refer to
L. Holm & C. Sander (1998) Removing near-neighbour redundancy from
large protein sequence collections. Bioinformatics 14, 423-429
Ramu
______________________________
Chenna Ramu; EMBL; Meyerhofstr. 1, 69117 Heidelberg, Germany
Email: chenna@embl-heidelberg.de
Url: http://www.embl-heidelberg.de/~chenna/
Tel: (49) 6221 387530 (Off) ; Fax: (49) 6221 387517
______________________________
On Thu, 12 Jul 2001, Quoc-Dien Trinh wrote:
> I have a medium selection of protein sequences (about 500) and I wish to
> eliminate redundancy. The only method I have thought of so far is to blast
> each sequence vs a Blast db created with this selection, and proceed to
> eliminate everything of threshold < 0.02 (using BioPython, of course).
>
> Of course, this method is rather long and fastidious; I wonder if anybody
> has a better solution to my problem (using BioPython or not).
>
> Thank you for your time,
>
> Quoc-Dien
>
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> | Quoc-Dien Trinh || quoc-dien.trinh@umontreal.ca |
> | Tel.: (514) 481-2808 || Université de Montréal |
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