Mapping motifs on one DNA strand only

Eric Schoonejans 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.

                some deleted

> >   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
                                                  ^ graphically
> >   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).

Thanks again

Eric Schoonejans
Institut des Sciences Vegetales CNRS - Gif sur Yvette - France




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