Bioperl: GSC perl modules

Ian Korf
Fri, 20 Mar 1998 09:56:00 -0600

Ewan's note about the Sanger perl modules reminded me that I ought to be
interacting with people about the perl modules I'm developing at the GSC
(Washington University, Genome Sequencing Center). Some of it is pretty
GSC-specific in design, but I'm trying to generalize as much as possible.

The modules are called Bio::GSC, and documentation can be found at:

Some interesting features include:
* A universal sequence markup model - unifies many aspects of sequence features
  so that a any program can be displayed, serialized, compared, dumped etc. in a
  common format.
* Markup filtering - eg. give me those features that have (x or y) not Z.
* Markup clustering - eg. don't give me anything too similar to something else
* Object-oriented code - it's a 3-fold hit in speed, but there are good reasons
  for doing it (usability, maintainability, and not very compute intensive).

Any comments or suggestions are welcome. I'd like to cooperate with other
BioPerlers if possible, so please contact me.

-Ian Korf
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