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. The way i did it was to create a .dat file of patterns
> like
>> 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
> sequence?
> (Mac, VMS, Unix or PC; GCG or freeware only).
You can use the same pattern file with findpatterns which has a command line
option -onestrand
Not graphical, but you get the positions.
--
------------------------------------------------------------------------
Peter Rice | Informatics Division
E-mail: pmr at sanger.ac.uk | The Sanger Centre
Tel: (44) 1223 494967 | Hinxton Hall, Hinxton,
Fax: (44) 1223 494919 | Cambs, CB10 1RQ
URL: http://www.sanger.ac.uk/~pmr | England
