help: abstract genome - gene finder

Raf rafta4NO^spam at hotmail.com
Thu Feb 26 10:37:40 EST 2004


ok, tnx for your quick reply :)

"Gordon D. Pusch" <g_d_pusch_remove_underscores at xnet.com> wrote in message
news:gi8yiq0y2b.fsf at pusch.xnet.com...
> "RaFTa" <rafta4NO^spam at hotmail.com> writes:
>
> > we've got an assignment from school to identify relevant parts of an
> > artificial genome, relevant parts being the genes.  we've searched on
> > google for gene-finding programs, but they always need the type of
> > species that genome belongs to...
> >
> > does anybody know a program that can handle this problem?
> >
> > we're informatics-student, so we dont really know a lot of the
> > biotechnology-world :)
>
> If your "fake" genome has been built out of genes taken from from species
> whose codon usages are not too dissimilar, you might try GLIMMER,
> <http://www.tigr.org/software/glimmer/>. However, if the "fake" genome
> has been built from a random "mix-and-match," about the only thing that
> _might_ work would be extract all of its "Open Reading Frames" (ORFs)
> that are long enough to plausibly contain genes (e.g., > ~120 bp),
> translate them, and then BLAST them against a non-redundant protein
> database...
>
>
> -- Gordon D. Pusch
>
> perl -e '$_ = "gdpusch\@NO.xnet.SPAM.com\n"; s/NO\.//; s/SPAM\.//; print;'





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