[BiO BB] How to find the same proteins?

[Mike Marchywka]

Also, they do offer specific utilities for blast:

http://www.ncbi.nlm.nih.gov/blast/docs/netblast.html

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-----Original Message-----
From:
bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformatics.org
[mailto:bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformati
cs.org]On Behalf Of Pankaj
Sent: ThursdayMarch-23-2006 05:15 AM
To: The general forum at Bioinformatics.Org
Subject: Re: [BiO BB] How to find the same proteins?



For this u can go to NCBI BLAST page and go to BLASTP. There u can paste ur
sequence and select PDB as the database to query. Just click on BLAST and u
get all seq similar to ur sequence. Filter out the results to find PDB ids
>99% similar to ur protein.
Sine u have 200 proteins u can download NCBI database and run local BLAST also.
Cheers 
Pankaj Khurana
Research Scholar
National Institute of Immunology
New Delhi
India
--
Open WebMail Project (http://openwebmail.org)


---------- Original Message -----------
From: Semen Esilevsky <yesint4 at yahoo.com>
To: bio_bulletin_board at bioinformatics.org
Sent: Thu, 23 Mar 2006 01:30:58 -0800 (PST)
Subject: [BiO BB] How to find the same proteins?

> Dear all,
> I'm a novice in bioinformatics and this question is
> probably stupid, but...
> I have a list of ~200 PDB id's. For each of them I
> have to build a list of all entries in PDB, which
> represent the same protein (say, >99% sequence
> similarity and no large gaps). Could someone suggest
> me the least painfull way of doing this?
> As far as I understand all what I need is the database
> where all pairwice BLAST allignments of PDB chains are
> stored. I've found one as a part of a PISCES server,
> but it is incomplete and contains some internal
> inconsistensies. Could someone suggest me a better one
> or there is a simpler way out?
> 
> Best,
> Semen
> 
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------- End of Original Message -------

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