[Bioperl-l] Reconstructing BLAST output

Jason Stajich jason.stajich at duke.edu
Thu Oct 28 15:15:55 EDT 2004

See Bio::SearchIO::Writer::TextResultWriter and HTMLResultWriter which 
reconstitute a report based on Bio::Search objects.  You will need to 
build Bio::Search objects however from the DB - something that I am 
sure has been done in part somewhere already.  Ensembl also has their 
own way to store this data but I don't think are using Bio::Search type 
object for it at the moment.

If someone gets this bit of to-from RDMBS code working for would be 
really nice to have it in bioperl as just a simple component.   I know 
lots of people have their own store-similarity-search-results schemas 
out there, happy to see a Bio::Search serializiation layer written to 
talk to these.

On Oct 28, 2004, at 11:36 AM, Adam Woolfe wrote:

> Hi,
> I was just wondering if there was any module in bioperl that can
> reconstruct BLAST output from the constituent data. I have parsed BLAST
> output using SeqIO into a relational database (so I have all the
> constituent data), but now i need to print
> that data back out to look like BLAST output. I know it sounds crazy 
> but
> thats what i need.
> cheers
> adam
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Jason Stajich
jason.stajich at duke.edu

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