Mapping motifs on one DNA strand only
es at trefle.isv.cnrs-gif.fr
Tue Nov 22 14:42:18 EST 1994
In article <PMR.94Nov22155154 at staffa.sanger.ac.uk>, pmr at staffa.sanger.ac.uk
(Peter Rice) wrote:
> In article <es-221194135903 at mac301.isv.cnrs-gif.fr> es at trefle.isv.cnrs-gif.fr (Eric Schoonejans) writes:
> > I have been using mapplot (from gcg) to locate and visualise small motifs
> > in DNA sequences.
> > My problem and hence my question is that it will search both strands for
> > each motif, like it would do for restriction enzymes sites. When the motif
> > is self complementary, like ACGT, no problem, but when it is not, it will
> > actually map the motif plus all occurences of its complementary motif like
> > ATCG _and_ CGAT.
> > So, is there a way to manipulate the file of motifs or the program to avoid
> > this or is there any alternative to display occurences of motifs on a DNA
> > sequence?
> > (Mac, VMS, Unix or PC; GCG or freeware only).
(Or Staden package, by the way)
> You can use the same pattern file with findpatterns which has a command line
> option -onestrand
> Not graphical, but you get the positions.
I forgot to mention that I _need_ a graphical display (to eye detect and
visualize non random distribution of the motifs along the sequence).
Institut des Sciences Vegetales CNRS - Gif sur Yvette - France
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