[Bioperl-l] From PDB to get nucleotide sequences for all related genomes?

"최상철" goshng at naver.com
Tue Oct 12 10:03:42 EDT 2004

Dear Bioperl Guru:

I'm Sang Chul Choi, a graduate student in the program of bioinformatics at NCSU.
I'm interested in Protein Evolution Modeling and recently I should apply a 
model to all PDB entries. The problem is that I am stuck in getting nucleotide
sequences of all related genomes for each PDB entry. 

There is "DBREF" section in PDB like this:
DBREF  1T7S A   74   210  GB     17507755 NP_491893       74    210
DBREF  1T7S B   74   210  GB     17507755 NP_491893       74    210
DBREF  1T9F A   22   206  GB     17508635 NP_491320       22    206
DBREF  1TC3 A    1    21  PDB    1TC3     1TC3             1     21
DBREF  1TC3 B  101   120  PDB    1TC3     1TC3           101    120
DBREF  1TC3 C  202   252  GB     1086778  P34257           2     52

And, I know that there is the source orgarnism section.

Using these two kinds of information, I have tried to get nucleotide sequences
from Database: NCBI, SWISSPROT, ...

Is there any good suggestion for this thing? Any comment will be helpful.


Sang Chul

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