Bioperl-guts: codon usage?

Gordon D. Pusch pusch@mcs.anl.gov
Wed, 15 Sep 1999 14:40:28 -0500


Andreas Matern <alm13@cornell.edu> wrote:

> I was trolling through some bioperl guts stuff when I came across a
> thread re:codon usage in bioperl (appended).  Is anyone working on
> such a pm?  It would be extremely valuable....

I am currently working on scripts to efficiently compute and
manipulate such statistics, as well as Bayesian estimator and
decision-theory algorithms to detect such ``spelling changes.''
Unfortunately, they are mostly ``stand-alone'' scripts, rather
than BioPerl-type OOP-modules, since I am not yet comfortable
with the OOP style (I am a physicist by training, so prior to 
a couple years ago, I wrote everything in <*!blech!*> FORTRAN... :-(

I am trying to learn how to code in the the OOP style, but am finding
the learning-curve almost unclimbable, and so far have not had time 
to actually practice coding it --- I have a VERY tight crisis-schedule,
and WAY too many of the items on my plate absolutely positively =HAVE= 
to be done CRUDELY by YESTERDAY, rather than elegantly by next month... :-(


Gordon D. Pusch                     |  Internet: <pusch@mcs.anl.gov>
Math and C.S. Div., Bldg.221/D236   |  FAX:      (630) 252-5986
Argonne National Laboratory         |  Phone:    (630) 252-5195 (Off)
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Disclaimer:  I'm a consultant collaborating with Argonne researchers;
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