[Bioperl-l] Categorization of EST's by species/taxonomy/lineage

[Paulo Almeida]

You say that because it wouldn't work, or because of all the blasts? My 
idea was that it would only be necessary to do one blast per species (or 
maybe a few, depending on the database's nomenclature being consistent 
or not). In any case, your solution is obviously better, I'm just curious.

-Paulo

Jason Stajich wrote:

>ugh - I hope you are not really going to do this... - I'll post code which
>should work with Bio::DB::Taxonomy as this was what it was intended to do.
>
>-j
>On Thu, 29 Apr 2004, Paulo Almeida wrote:
>
>  
>
>>Perhaps a little far fetched, but what if you write a script that goes like:
>>
>>Read sequence from flat file.
>>If it's from a new species,
>>    Blast against mRNA database AND species database
>>    Check hits until you get one with the full lineage
>>End if
>>Sort it based on the lineage
>>
>>I'm suggesting that only based on what you said, about mRNA records
>>tending to have the full lineage, I have no idea if it would work. To
>>blast against mRNA for the desired species you would add something like:
>>
>>$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = '$species [ORGN] AND biomol_mrna [PROP]';
>>
>>
>>-Paulo Almeida
>>