[Bioperl-l] Code to contribute

Michael Janis mjanis at chem.ucla.edu
Thu Aug 14 19:37:05 EDT 2008



I've had some perl code lying around for what seems like forever and I'd
like to contribute it to bioperl, if such facilities don't already exist in
bioperl.  The code implements shuffling (DNA or RNA) keeping the
dinucleotide composition (and codon usage) intact through a Eularian path
approach as described in Altschul and Erickson (1985).  The code seeds the
Eularian paths by keeping the first and last nucleotide invariant in the
shuffle - which has minimal detrimental effects to the purpose of the
algorithm, in my experience.


A quick search on the bioperl website shows that there is a mutation.pls
script, and facilities for using Sean Eddy's SQUID C library, which
implements the same function (I wrote this particular function before I knew
how to use C).  As such, it's probably not as elegant as Sean Eddy's
implementation, but it works - and it's entirely in perl.


The bioperl developer pages suggest a post to the mailing list as the best
place to start contributing to bioperl.  Is this a useful function to add to
the project?


Best Regards,





Michael Janis

 <mailto:mjanis at chem.ucla.edu> mjanis at chem.ucla.edu



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