Please excuse this hastily thrown together home page. The project page is at: http://sourceforge.net/projects/compbio/ or you can go directly to the cvs tree.
CompBio is intended as a restricted set of methods that I found I used over and over again in my work. Basically there is a set of sequence format transformations, such as fasta to table (tab delimited), dna to amino acid translation (including six frame) and a simple interface to runnning WUBlast and basic parsing of the output.
The Simple module is intended to provide a flexible, object oriented interface to the methods in CompBio. Hopefully this will lower the barrier to inexperienced perl programmers to make use CompBio. It also should make it easier for any developer to plug a method into existing code without having to change formats or data containers in most cases.
Real progress has finally been made on the DB module. Some sample schemas are available with some early documentation on creating the databases under MySQL. The results of my first attempts to use it were very encouraging.
There is a mailing list available for users and one for announcements
CompBio is also available on the CPAN: http://www.cpan.org/authors/id/S/SE/SEANQ/
Please email me with any questions or suggestions seanq@molbio.mgh.harvard.edu
Thanks, TTFN,
Sean