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

Chris Fields cjfields at illinois.edu
Wed Aug 11 17:07:20 EDT 2010


For some reason I thought there was a more up-to-date one somewhere.  Ah well, can't keep track of all the code in bioperl :>

chris

On Aug 11, 2010, at 4:05 PM, Scott Cain wrote:

> 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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>> 
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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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