[Bioperl-l] parsing xml output

[Hubert Prielinger]

hi warren,
that means if I alter the DTD (if that is possible) by adding the 
taxonomic id to the DTD..... then I should have the taxonomic id tag in 
the xml file (theoretically)
but I guess this is only possible with a local search (blastall) but not 
with an online search.

greetings

Warren Gish wrote:
>
> On May 19, 2006, at 11:52 AM, Hubert Prielinger wrote:
>
>> 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
>>
> The taxonomic id is not an entity in the NCBI XML DTD.  If the 
> information was embedded in deflines, one could conceivably parse for 
> it, but I believe the NCBI only distributes taxids in their ASN.1 data 
> and in their pre-formated BLAST databases, and NCBI BLAST only reports 
> taxids in its ASN.1 output format, where taxid is available as an entity.
>
> --Warren
>
>