intron splice-junctions software

Marc Champagne M.Champagne at nospam.cellbio.duke.edu
Mon Aug 18 08:35:12 EST 1997


In article <33E8B635.4368 at rug.ac.be>, Van Geldre Els
<Els.VanGeldre at rug.ac.be> wrote:

> Dear all,
>   
>   First of all I would like to thank you for all previous answers and
>   suggestions to my questions. Secondly, I would like to ask you the
>   following. Does someone know wether there exists (and where I can find
>   it) a program that is capable to find splice junctions in a given gDNA
>   sequence ? I have some PCR products derived from gDNA of plants (about
>   1kb). I would like to derive the protein sequence from these DNA
>   sequences, but only the exons without the introns. I found such a
>   program specific for Arabidopsis, but I wonder wether there exists 
> something
>   more general for other plants.
>   
>   Thank you for answering,
>   Els

Your first stop should definitely be the Genefinder www page, look up the
Baylor College of Medecine homepage.  They have intron/exon broder tracking
algorithm, and it can detect a lot of them.  

Within a few months, i will have a www page available that does a codon bias
analysis.  We now have a unix version that runs pretty well, it has helped many
people here at Duke to 1-find coding region 2-detect reading frame slip in 
coding region 3-find coding/non-coding regions in nucleotide sequences.  It's
based on the fact that in each organism, some codons for a given aminoacid are
'chosen' more often than other.  By plotting this bias, one can usually detect
coding from non-coding regions.  

Good luck,

m.champagne at cellbio.duke.edu

-- 
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