[Bioperl-l] ORF identification/prediction

Hilmar Lapp lapp@gnf.org
Mon, 08 Jan 2001 14:55:10 -0800

Jason Stajich wrote:
> To the best of my knowledge, we don't currently have bioperl modules that
> predict/identify (depending on your confidence in the software =) Open
> Reading Frames. Eric and I were thinking of working on a bioperl module
> for this.  Any suggestions, known pitfalls, etc are welcomed.

There is the Bio::Tools::ESTScan module, which obviously relies
on ESTScan as the ORF predicting external tool. If you plan to
implement a full-fledged ORF prediction algorithm in perl that
module is not what you want. (BTW ESTScan consists of a driver
layer in Perl; the core of the algorithm is written in C. One
could try to integrate/rewrite the driver layer into/in Bioperl.)

Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757