ORF finder? - ORF finder? (Jun/09/2005 )

There are many programs that will find open reading frames (ORFs) (start codon->stop codon) in a given sequence.

However, the first ATG used to create the ORF may not be the correct start codon - it may be one further into the sequence.

Does anyone know of a program that will return ALL of these potential ORFs - that might be termed "ORFs within ORFs"?

Please post or email if you know of anything suitable - maybe someone has written a BioPerl program to do this?

thanks in advance,

LB

If you click on "six frames" in the NCBI Orf Finder, it will indicate the possible start codons in each frame (in blue). Note that the start need not be ATG, but can be TTG or GTG (not usually CTG).
I believe there is a button on orf finder to turn on alternative initiation codons.

QUOTE (phage434 @ Jul 12 2005, 03:20 AM)

Note that the start need not be ATG, but can be TTG or GTG (not usually CTG).

Are these TTG and GTG also the start codons for the eukaryotes? I never heard of it.

Alternative starts are for prokaryotes.

Yep,

Frameplot 2.3.2

http://www.nih.go.jp/~jun/cgi-bin/frameplot.pl

Let's you choose what start codon you want, along with other nifty features.

Have fun!

Nicole