[Pipet Devel] BlastXML

david.lapointe at umassmed.edu david.lapointe at umassmed.edu
Sun Jan 24 15:30:58 EST 1999

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.

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


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.


More information about the Pipet-Devel mailing list