[BiO BB] PDB sequence --> coding sequence

[Taylor, Deanne]

Iddo: 

Apologies if you already know some of this stuff (in advance). :)

My suggestion is to use tblastn.  You can search with your fragment at BLAST
at NCBI; though your fragment may have several intronic sequences removed,
sometimes BLAST can match parts of your protein to different DNA regions.
There are several flavors of BLAST available but you want tblastn. Go to

http://www.ncbi.nlm.nih.gov/BLAST/

and select "Protein query -- translated db [tblastn]" under the Translated
BLAST searches. tblastn
is for comparing a protein query against a nucleic acid database (the
nucleic acid database sequences are translated into all six reading frames
and then compared to the protein query sequence).

If tblastn doesn't work for you, write back, I might have links to various
other things that might be of use, but none so convenient as a web
interface. :) A good place to look for that kind of thing yourself is
Pedro's bioinformatics tool list:
http://www.public.iastate.edu/~pedro/rt_1.html

Good luck! 

Deanne

-----Original Message-----
From: Iddo Friedberg [mailto:idoerg at cc.huji.ac.il]
Sent: Thursday, February 15, 2001 4:45 AM
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] PDB sequence --> coding sequence


Hi all,

(Question originally posted to the "Ask the Open Lab" forum. I'm reposting
it here, hopefully something will arise).

Does anybody know of some way to get the coding sequence given a sequence
from PDB? As you may very well know, PDB sequences are usually partial,
fragmented versions of the actual protein sequence. Sometimes with
mutations inserts (OK, so I cannot get the coding sequence for mutation
inserts, for obvious reasons). Collating this data via automatic means
seems rather cumbersome.

Any help, including pointers to an appropriate database, scripts
repository, or any kind of forum with people who might be able to answer
this would be useful.

Thanks,

Iddo Friedberg

--

Iddo Friedberg                                  | Tel: +972-2-6758647
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email:
idoerg at cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |
http://bioinfo.md.huji.ac.il/marg/people-home/iddo/


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