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