[Bioperl-l] A problem parsing BLASTX 2.2.8 reports

[Gilles Parmentier]

Hi all,

Using mac os X I noticed a lot of problems with 2.2.8. reports. In fact 
they look really buggy (strange query lengths among other things). 
Bioperl::SearIO is not able to parse them. To tackle this I downgraded 
my install to 2.2.6 :(

Gilles

Jason Stajich wrote:

>Matt - I'm having a little trouble understanding the problem - why aren't
>the value you are reporting what you expect.
>
>With BLASTX the query will have a frame (0,1,2) in GFF/bioperl not
>(1,2,3). So in your example the query will have some frame [1] and some
>strand [1] since frame is '+'.  The hit will have no strand since it is
>protein [0].  Isn't that what you got?
>
>$hit->frame is going to return something different depending on what type
>of search you did also.  For TBLASTN or BLASTX it will return the valid
>frame for whatever makes sense (hit or query) and will return an array for
>TBLASTX.
>
>Also, the Hit object will try and make a summary value for all the HSPs -
>this will be the frame for all the HSPs (if they share the same frame
>throughout) or just the frame of the first HSP if they differ.
>
>I don't really like to rely on this personally.  Rather I would call it
>explicitly for the HSP:
>
>$hsp->query->frame or $hsp->hit->frame
> or
>$hsp->frame('query'), $hsp->frame('hit')
> or
>my ($qframe,$hframe) = $hsp->frame;
>
>All in all it is hard to say without a copy of the report(s) and your
>code.
>
>-jason
>
>On Tue, 30 Mar 2004, Matthew Links wrote:
>
>  
>
>>I have run into a problem parsing BLASTX reports (version 2.2.8). When I
>>ask for strand and frame on the Bio::Search::Hit::HitI object I am
>>getting back the wrong answer.
>>
>>I think this has to do with a slight formatting change in the BLAST
>>output.
>>
>>--- BLASTX 2.2.5 ---
>>
>>    
>>
>>>gi|19879878|gb|AAM00191.1| guanine nucleotide-exchange protein GEP2
>>>      
>>>
>>            [Oryza sativa]
>>          Length = 1789
>>
>> Score =  320 bits (819), Expect(2) = 7e-98
>> Identities = 160/193 (82%), Positives = 173/193 (89%)
>> Frame = +2
>>
>>--- BLASTX 2.2.8 ---
>>
>>    
>>
>>>gi|38346787|emb|CAE02205.2| OSJNBa0095H06.12 [Oryza sativa (japonica
>>>      
>>>
>>            cultivar-group)]
>>          Length = 1724
>>
>> Score =  102 bits (254), Expect = 5e-21
>> Identities = 62/204 (30%), Positives = 103/204 (50%), Gaps = 30/204
>>(14%)
>> Frame = +2
>>
>>In my debugging it looks like everything is ok except for the
>>strand/frame data. Which when parsing 2.2.8 gets
>>
>>hit->frame = 1
>>hit->strand('query') = 1
>>hit->strand('hit') = 0
>>
>>Has anyone seen this problem before?
>>
>>Thanks in advance,
>>
>>Matt
>>
>>
>>    
>>
>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu
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>  
>

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