[BioPython] Eliminating redundancy : how?

[Ramu Chenna]

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
>
>  ===========================================================
> | Quoc-Dien Trinh         || quoc-dien.trinh@umontreal.ca   |
> | Tel.:  (514) 481-2808   || Université de Montréal         |
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