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

Ann Loraine aloraine at gmail.com
Sun Sep 17 17:39:45 EDT 2006


Thanks!

-Ann

On 9/17/06, Diego Martinez <sariego9 at yahoo.com> wrote:
> 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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>
>
>
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-- 
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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