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

[Diego Martinez]

Hello, 

There is also the SEALS package from Koonin's group at NCBI,
we use that alot.  it has a bunch of command line tools, I believe it 
is all in PERL, so you can gut it and reuse.

http://www.ncbi.nlm.nih.gov/CBBresearch/Walker/SEALS/

if you are looking at ESTs, you may also want to look at estscan,

http://www.ch.embnet.org/software/ESTScan2.html

or there is a genewise like est Gene modeler tool the Wise2
package by Birney and Durbin that you may want to look at.

Diego
 


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----- Original Message ----
From: Ann Loraine <aloraine at gmail.com>
To: General Forum at Bioinformatics.Org <bio_bulletin_board at bioinformatics.org>
Sent: Sunday, September 17, 2006 1:19:38 AM
Subject: [BiO BB] command-line (scriptable) ORF finders?

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.

(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?

I've found a variety of web sites that claim to do this, but, as you
know, Web sites don't really cut it when you are working with
thousands of sequences. And also, I would like to see the code in case
I run into problems.

Any thoughts or suggestions (other than pointers to Web tools, please)
would be greatly appreciated!

Sincerely,

Ann Loraine

-- 
Ann Loraine
Assistant Professor
Section on Statistical Genetics
University of Alabama at Birmingham
http://www.ssg.uab.edu
http://www.transvar.org
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