Plasmidb

This release has more integration of DNA to protein sequences; DNAs
are automatically translated to give protein sequences, and
ProtParam-type information is generated from it. It has a simplified
data model, more auto-calculated statistics, and improved BioPHP.

Plasmidb was meant to make interaction between biological sequences stored in the database with bioinformatics tools seamless. This release provides an idea of what the DB can and should do. In this release, molecular weights are calculated from DB protein and RNA sequences. On the Primer page, selecting each oligonucleotide produces output of the protein for which it encodes. More analyses of this type will follow.

This release has been extended to include translation of DNA sequences, calculation of primer melting temperatures, whitespace stripping, and formatting. Other utilities include molecular weight calculation of products and a primer designer for automated cloning of multiple genes in a systematic fashion.

Session handling now works more reliably, but can be turned
off in the configuration file. Bio::PHP support for translation
of DNA->protein sequences has been started and is included
in the distribution.

Improvements were made to the library, session management, and HTML display of links. The interface files were updated to work with the new classes.