[Biojava-l] biojava.dp doc/tutorials?

[Matthew Pocock]

Hi Rik,

I hope that UCSD is having better weather than we are. England seems to
be totaly below water at the moment.

"Richard K. Belew" wrote:

> mr. matthew pocock and biojava,
>
> i'm contemplating using the dp example
> as the focus for a project in a CS data structures
> class will be teaching with a bioinformatics

*blush*

>
> spin.  might anyone else have done
> something similar, or developed other materials
> motivating the code?  i find the author 'Samiul Hasan'
> in one source file, but don't know how to contact
> him either?  thanks for any help,

The DP objects have changed a bit since the 1.01 release - and for the
better. We should put up a new snapshot of the project on the web-site
as soon as I fix a show-stopper bug in the alphabet indexing code. The
DP stuff was designed from the ground-up to be primarily a data
structure. For pair-wise DP, there is now an interpreter object that
performs alignments by 'interpreting' the HMM, and I have in development
(but not CVS) a compiler that 'compiles' the HMMs to java byte-code
which should be faster & produce bytecode that is *very* optimizable by
hotspot.

I have used the HMMs to model various biological sequences, and found
them to be very flexible. They may be prohibatively slow on some older
VMs for high-throughput, but for testing architectures & training
models, this speed penalty is more than out-weighted by the ease with
which you can build your particular model.

There is sadly almost no tutorial documentation. I think that Samiul is
interested in writing some. He has been using the package to model
histone binding sites, and I think he is the nearest persone we have to
a user (as oposed to developer) at this time.

Please feel free to bother me at any time about how the code works, why
it looks like that, or tell me of any difficulties/bugs. I hope that it
ends up being useful as a teaching aid for your class.

All the best,

Matthew

>
>
>         rik
>
> --
> Richard K. Belew                          rik@cs.ucsd.edu
>                               http://www.cs.ucsd.edu/~rik
> Computer Science & Engr. Dept.
> Univ. California -- San Diego       858 / 534-2601
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