[Pipet Devel] BlastXML

[david.lapointe at umassmed.edu]

Ok, I am one of those weasels too. I am not suggesting moving to Java but
here's a piece that came down the BioWidget pipeline this week.

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January 19, 1999

PharmTools SDK Suite(TM) (Early Access 1)

Announcing the availability of PharmTools SDK Suite(TM) (Early Access 1)
from WorkingObjects.com for evaluation. PharmTools SDK is a collection
of reusable Java frameworks and toolkits for use in the development of
bioinformatics applications. This early access release includes: the
Blast Parsing Framework and BlastXML-SDK. The Blast Parsing Framework is
a set of design patterns and Java classes for processing native (i.e.,
local) and NCBI website generated Blast2 reports. BlastXML-SDK extends
the Blast Parsing Framework functionality to support the creation and
processing of BlastXML documents.

The PharmTools SDK Suite may be downloaded from the WorkingObjects.com
website at
http://www.workingobjects.com.

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It's pretty large, about 100 kb of *.jar for the application, and 500 kb for
the sdk.jar with a blastxml.dtd.  It has a functionality that relates to
some discussion we had earlier this week on parsing the output of programs,
which incidently is made easier by perl (regex).  Many authors of *new and
improved* programs, ie FASTA, have included parsible output into their
programs.  This makes it easier to connect different analyses. IMHO a good
thing.  Most MolbBio packages that I have seen are just a bag of unrelated
pieces. meaning you can't run the output of BLAST or FASTA into CLUSTAL
without a bit of work.

David