[BiO BB] command-line (scriptable) ORF finders?
landman at scalableinformatics.com
Sun Sep 17 13:39:10 EDT 2006
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
> (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?
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web : http://www.scalableinformatics.com
phone: +1 734 786 8423
fax : +1 734 786 8452 or +1 866 888 3112
cell : +1 734 612 4615
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