Programatically accessing RCSB-PDB
1
0
Entering edit mode
9.4 years ago
Bioaln ▴ 360

Hello. I've recently discovered RCSB already offers exactly what I need. SOme PDBs also have list of corresponding SNPs.(sequence/annotations/SNP). The problem is the following. I have way to many PDB accessions to manually download corresponding SNPs. Is there any way I could programatically access this site?

So to make things more clear, what I'm looking for is a way to in one script/program download for example

PDB: 4HHB AND its SNPs:

rs41486646 change: S-P
rs28928886 change: K-N
rs63749948 change: A-D
rs41497846 change: S-Y
rs63749791 change: L-V
rs41514946 change: S-R
rs41491146 change: F-L
rs33910377 change: P-LR 
..

I need just accession numbers (rs..). Can this be done?

Thank you for help

SNP pdb • 1.5k views
ADD COMMENT
0
Entering edit mode
9.4 years ago
Bioaln ▴ 360

I found something similar in the RCSB database dump!

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

ADD COMMENT

Login before adding your answer.

Traffic: 1613 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6