Mapping motifs on one DNA strand only

Peter Rice pmr at staffa.sanger.ac.uk
Tue Nov 22 10:51:54 EST 1994

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

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