[Bioperl-l] Variation

Stefan Kirov skirov at utk.edu
Tue Apr 27 10:01:43 EDT 2004

Do you know who is working on the bioperl access to ensmart?

Heikki Lehvaslaiho wrote:

>We do not have a way to access dbSNP. Maybe we should...
>Bio::Variation objects do not retrieve anything. They are plain storage 
>objects. Currently the only way to create them automatically is using 
>Bio::LiveSeq modules which read an EMBL/GenBank entry to create a gene model 
>which is then mutated and results written out in a Bio::Variation::SeqDiff 
>object. See examples/liveseq/change_gene.pl.
>You could access this information using Ensembl code base which is based on 
>bioperl, but it is not easy. I can only repeate what I posted last week that 
>bioperl access to EnsMart is a good idea and hopefully will be available at 
>the end of summer.
>	-Heikki
>On Tuesday 27 Apr 2004 12:36, Jonathan Manning wrote:
>>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

Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
1060 Commerce Park, Oak Ridge
TN 37830-8026
tel +865 576 5120
fax +865 241 1965
e-mail: skirov at utk.edu
sao at ornl.gov

More information about the Bioperl-l mailing list