[Biojava-l] NetBlast for java?

[ozborn@UVic.CA]

On Fri, 15 Mar 2002, Guoneng Zhong wrote:
> Is there such a thing as java class that does blast search remotely or
> locally?  I know there are report parsers, but I don't see any that does
> the report creating.
>
Since Blast is pretty much available for every platform, the easy thing is
probably to run that version and parse the output of the resulting file
which more or less looks identical to a standard blast file.  That's what
I do anyway.

I also a question.  What is the best way to start using biojava?  I have
lurked on this list for over a year, but the project I am working on
doesn't use biojava at all, although there are many places it could.  (My
project is a poxvirus database for the Center for Disease Control,
although it will eventually hold information on other viruses, and
possibily bacteria).

Right now the database only has complete genomes, genes, and gene families
but no sequences.  I want to add bio-java sequences to the database, and
features which is also not there (it's all in the "genes" table).  The
problem is I don't really know how all the packages in biojava fit
together, or where to just start using it in a productive way.  Do I just
use bio.seq.db?  From what I have looked at, I can't really see the
advantage of doing so at this point.  Can anyone give me some pointers on
getting started?

 -John