Bioperl-guts: codon usage?

Gordon D. Pusch
Wed, 15 Sep 1999 15:08:36 -0500

Andreas Matern <> replies:

> If you wouldn't mind sharing your stand alones (especially if they
> are stand alones written in Perl) I think the bioperl community
> would be enriched by them, and (with your permission) we can link to
> them on:

They are certainly written in perl --- I don't write ANYTHING in any other
language (except English), nowadays! 8-)  And I will be happy to post them
once I'm done working on them. 

Unfortunately, however, they're being written for a crisis that's a couple
levels down on my Maslov-hierarchy, so it's likely to be several weeks to
a month before they're polished enough to be ``ready for prime time''... :-(

BTW, I am =VERY= much interested in replacing my current hash-based kmer-use
tables with a suffix-tree implementation at some point in the near future,
to facilitate replacing my current fixed-order Markov-chain DNA-model with
a variable-order Markov Random Field model. If anyone on this list is working
on or knows of a good suffix-tree module, I would very much appreciate a
pointer (or even a handle! :-) to it...

Thanks in advance,

Gordon D. Pusch                     |  Internet: <>
Math and C.S. Div., Bldg.221/D236   |  FAX:      (630) 252-5986
Argonne National Laboratory         |  Phone:    (630) 252-5195 (Off)
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