[Bioperl-l] Variation

wangqi wangqi at seu.edu.cn
Tue Apr 27 10:41:42 EDT 2004

There may be another method to get the 'founction ' infromation from dbSNP, You can get the dump the compress file of  'function' infromation through NCBI ftp server. It may be ftp.ncbi.nih.gov/snp/mssql/data/SNPContigLocusId.bcp.gz , you can download it and uncompress it in your loacl harddisk. It is a text file and you can use a rs number to search the related 'function' information of snp. 

Wang Qi 

Hello Bioperlers!

Could someone save me some time and tell me if it's possible to access
NCBI variation databases using bioperl? I've parsed the 'Variation'
feature information from GenBank files, but would like to get
information such as the 'function' you can see at dbSNP- i.e.
synonymous, nonsynonymous etc. I can't see this information anywhere in
the Bio::Variation objects, though that could be me being a bit dense.

Also, the following test code (with a valid dbSNP number) doesn't work-
any idea why?

$seqDiff = Bio::Variation::SNP-> new(-id=>  2256408);
$ori = $seqDiff-> aa_ori();
$mut = $seqDiff-> aa_mut();
print "$ori $mut \n";



Bioperl-l mailing list
Bioperl-l at portal.open-bio.org


More information about the Bioperl-l mailing list