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

Paulo Almeida paulo.david at netvisao.pt
Mon May 3 09:20:53 EDT 2004

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.


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.
>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

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