Bioperl: Finding ORF's

[David J. States]

We been working on improving the accuracy of ORF definition, although it is
not part of bioperl at present.  See http://www.ibc.wustl.edu/~zkan/CDS/
The strategy is basically an extension of the work that Agarwal and Bafna
presented at RECOMB with more detailed models for the initiation sites.

David

P.S. Be cautious when using GenBank annotation.  Many of the sites in
GenBank have not been experimentally verified, and there are often grounds
for questioning the annotated initiation site such as closely related
homologs with a different (and conserved) ATG.


----
David J. States, M.D., Ph.D.
Associate Professor and Director
Institute for Biomedical Computing
Washington University in St. Louis
700 S. Euclid Ave.
St. Louis, MO   63110

tel: 314 362 2134
fax: 314 362 0234
email: states@ibc.wustl.edu



On Thursday, July 15, 1999 10:21 AM, James Diggans
[SMTP:jdiggans@genomics.biotech.ufl.edu] wrote:
> Hello all, is there support within bioperl for tracking down open
> reading frames within sequences? I've given the docs a cursory search
> and can find nothing ... 
> 
> Thanks,
> James
> 
>
****************************************************************************
> *    James C. Diggans                 
> jdiggans@genomics.biotech.ufl.edu   *
> *    UF ICBR Protein Expression Core  
> http://genomics.biotech.ufl.edu     *
>
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