[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 17:05:25 EDT 2010


Um, yeah, it's in bioperl: bp_search2gff.pl.

Scott


On Wed, Aug 11, 2010 at 4:45 PM, Chris Fields <cjfields at illinois.edu> wrote:
> HMMER3 is parsed by Bio::SearchIO now in bioperl-live, and I think there is a generic SearchIO->GFF3 script floating around the intertubes somewheres...
>
> chris
>
> On Aug 11, 2010, at 3:38 PM, Doug wrote:
>
>> Hi Scott,
>>
>> Good idea. Would you happen to know of an existing HMMER3 to GFF3
>> converter?
>>
>> Thanks for your advice,
>> -- Doug
>>
>> On Aug 11, 4:16 pm, Scott Cain <sc... at scottcain.net> wrote:
>>> 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.
>>>
>>> Scott
>>>
>>>
>>>
>>>
>>>
>>> On Wed, Aug 11, 2010 at 4:11 PM, Doug <douglas.h... 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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>>>
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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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>>
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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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