intron splice-junctions software
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
> more general for other plants.
> Thank you for answering,
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.
m.champagne at cellbio.duke.edu
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Pls remove -nospam- from my address if you reply by e-mail
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