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

[Stefan Rensing]

Hi,

> (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.

We found FrameD to be superior to ESTScan and Estwise in predicting ORFs
in moss (P. patens). We are using species-specific (i)HMMs, repectively.
http://bioinfo.genopole-toulouse.prd.fr/apps/FrameD/FD
http://bioinfo.genopole-toulouse.prd.fr/apps/FrameD/Help/FrameDWeb_5.html

> (2) I am also looking for a tool that can take as input a set of exon
> annotations (or mRNA-to-genome alignments) and return the most likely
> CDS start and end for the given gene structure. Tools that can jigger
> the alignment/exon boundaries to optimize the ORF *and* which pay
> attention to codon usage rules would be extra great. This is for
> deducing novel gene structures from cross-species mRNA-to-genome
> alignments. Maybe there is a gene-finder that does this?

You might want to have a look at GenomeThreader,
http://www.genomethreader.org/, which allows spliced alignments using
non-identical mRNA/protein sequences (i.e., homologs from other species).

Cheers, Stefan


-- 
Dr. Stefan Rensing, Group Leader Computational Biology
Plant Biotechnology, Faculty of Biology, University of Freiburg
Schaenzlestr. 1, D-79104 Freiburg, Fon: +49 761 203-6974, Fax: -6945
http://www.plant-biotech.net/  http://www.cosmoss.org/
stefan.rensing at biologie.uni-freiburg.de

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