[Bioperl-l] How to store results of searches of translated DNA in SeqFeature::Store database of the original DNA?

Scott Cain scott at scottcain.net
Wed Aug 11 16:16:22 EDT 2010

Hi Doug,

I don't know if any of the things you've thought of would work; I've
never tried it.  My inclination would be to express your data in GFF3
and use the standard loader.


On Wed, Aug 11, 2010 at 4:11 PM, Doug <douglas.hoen at gmail.com> wrote:
> One possible answer to my own question: Use
> Bio::SeqFeature::PositionProxy's? Would this work?
> On Aug 11, 3:13 pm, Doug <douglas.h... at gmail.com> wrote:
>> Hi,
>> I am trying to store in a SeqFeature::Store database the results of
>> searches of translated DNA. The DB contains the original DNA
>> sequences. For instance, I have done HMMER searches of 6-frame
>> translations of the sequences stored in the DB. I want to store these
>> results "at" their (equivalent) DNA positions, which I can calculate.
>> Preferably, I would like to directly store the SeqFeature::Similarity
>> objects that I get from parsing these searches. But they are of course
>> located on different coordinate systems than the DNA, so I guess I
>> can't (or shouldn't) create a SeqFeature (e.g. Generic) at the correct
>> DNA position and then store the Similarity's as sub-SeqFeatures.
>> I could just set the Similarity's position to the (calculated) DNA
>> coordinates, or alternately make a new SeqFeature and copy in the
>> attributes I want. But is there a more elegant solution?
>> Thanks,
>> -- Doug
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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