[Bioperl-l] FW: ORF finder

Hilmar Lapp hlapp@gmx.net
Wed, 06 Sep 2000 14:06:22 +0200

"Gatherer, D. (Derek)" wrote:
> >>what sort of ORF finder would you be interested in? One that takes the
> >>sequence as it is and outputs the most likely ORF (based on length and
> >>coding potential)?
> A _very_ simple ORF finder that could scan a database of cDNAs, and print
> out all the potential ORFs and their putative translated products.
> >>A couple of weeks ago I wrote to the BioPerl list about ESTScan.....
> educated suggestion of how to model the insertions and deletions ESTScan
> predicts....
> Nothing so sophisticated, as yet!!
> Here's the code I have so far:


great, thanks for the code. Check it in in the development trunk (if you
haven't got CVS access yet, Ewan or I guess Chris will be happy to get
you one, I assume).

There are a couple of things that should be done in order to fit it into
the general BioPerl design:
1) Use Bio::Tools::CodonTable instead of hard-coding initiators and
2) Return SeqFeatureI implementing objects instead of multi-dimensional
arrays (these are very easily screwed or wrongly accessed, BTW).
3) Consider following the next_feature() layout, returning one ORF at a
time until input is consumed.

Apart from that, a test-script (look into the t/ directory to see how to
set up a test script) would be nice if not essential (without one, you
will be left alone with maintaining/improving your module, and a release
coordinator may decide to leave out your stuff).


Hilmar Lapp                                email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
A-1235 Vienna                                fax: +43 1 86634 727