[Bioperl-l] Variation

Stefan Kirov skirov at utk.edu
Wed Apr 28 09:36:11 EDT 2004

Well, actually I was thinking about contributing... I find Ensembl 
tremendously useful, but honestly the documentation is pretty bad. So 
bottom line making bioperl compliant access to ensembl should be quite 
useful. Can you let me know what the plans are (when there are some)? 
This way I will be able (probably) to help.

Heikki Lehvaslaiho wrote:

>Hmm. No-one at the moment, but I've got the feeling that once the API is 
>stable enough, I will be heavily involved in bioperlization of it. Mostly 
>because I have not kept my mouth shut but also because I think it is 
>The situation right now is that there is a java query interface to Mart and a 
>port of the functionality is under way to perl but is far from being 
>finished. Most importantly, it gives pretty generic query interface only 
>which does not link well to bioperl.
>If you have anything specific in mind, by all means ask, but I can not 
>quarantine I know the answer. 
>	-Heikki
>On Tuesday 27 Apr 2004 14:01, Stefan Kirov wrote:
>>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

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