I am optimistic about bionet.software.sources. Current copyright
laws sometimes discourage the general distribution of a software package
(lest it be considered in the public domain), there are a lot of things
that have been written that are not really big enough to warrant protection,
but very generally useful. One example is extractn/gbann, which is
in the public domain, and is used to extract sequences and annotations
from the compressed genbank format. (Unfortunately, when they changed the
annotation format, gbann broke.)
One of the things I would very much like to see would be a
general set of of programs for indexing/extracting sequences from any
standard database format. I find it very frustrating to have to
reformat databases or keep multiple copies, and have taught FASTA about
most popular formats. Unfortunately, although FASTA can read most
libraries, users are often frustrated because the software to extract
sequences is unavailable. I would happy to donate the code that we
use to index PIR/VMS format and Genbank flat file format (two separate
sets of programs) to get the ball rolling.
There are many other "little" problems that are could benefit
from this newsgroup.
Bill Pearson
