help: abstract genome - gene finder
Gordon D. Pusch
g_d_pusch_remove_underscores at xnet.com
Thu Feb 26 10:37:37 EST 2004
"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
-- Gordon D. Pusch
perl -e '$_ = "gdpusch\@NO.xnet.SPAM.com\n"; s/NO\.//; s/SPAM\.//; print;'
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