[BiO BB] command-line (scriptable) ORF finders?

[Joe Landman]

Hi Ann:

Ann Loraine wrote:
> Hello all,
> 
> I'm hoping someone on the list who is involved with EST or full-length
> cDNA sequencing projects can help me with something (well..two
> things):
> 
> (1) I am looking for a command-line, scriptable tool that can take as
> input an EST, cDNA, or assembled EST contig ("unigene") sequence and
> return the most likely or longest open reading frame. This is for a
> plant EST project.  It should also pay attention to codon usage rules.

Would getorf from EMBOSS help?
http://emboss.sourceforge.net/apps/cvs/getorf.html

Joe

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Joseph Landman, Ph.D
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