[Bioperl-l] parsing xml output

[Christopher Fields]

You'll have to pull the GI or accession from each hit and do a lookup by either 
grabbing the sequence and using Bio::Species or use Bio::DB::Taxonomy; there 
isn't any tax information directly incorporated into BLAST reports AFAIK.

Chris

---- Original message ----
>Date: Fri, 19 May 2006 10:52:28 -0600
>From: Hubert Prielinger <hubert.prielinger at gmx.at>  
>Subject: Re: [Bioperl-l] parsing xml output  
>To: Warren Gish <gish at watson.wustl.edu>, bioperl-l at bioperl.org
>
>hi,
>I wondered whether is it also possible in the xml output (either WU or 
>NCBI - Blast) to get the species (taxononmy) for every hit, if I do a 
>general search.
>regards
>
>Warren Gish wrote:
>> Right, the WU-BLAST tabbed output contains more fields.  (See http:// 
>> blast.wustl.edu/blast/tabular.html).
>> --Warren
>>
>>   
>>> Whoops - sorry Warren - for some reason I had it in my mind that it  
>>> was different.  So the blastxml parser should work fine.  The  
>>> WUBLAST tab-delimited output is different than NCBI's -m8/9 though,  
>>> right?
>>>
>>> -jason
>>>     
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>   
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l