I have been using mapplot (from gcg) to locate and visualise small motifs
in DNA sequences. The way i did it was to create a .dat file of patterns
motifA 1 ATCG 0 !
motifB 1 ACGT 0 !
etc..., which can be read by the program and it will then display a nice
plot of the occurences of the motifs.
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
(Mac, VMS, Unix or PC; GCG or freeware only).
Thanks a lot
Institut des Sciences Vegetales CNRS - Gif sur Yvette - France