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oligo frequency

Brian Fristensky frist at cc.UManitoba.CA
Thu May 11 16:57:38 EST 2000

Ahmed Fadiel wrote:
> Hi,
> I hope if some one provides me with a list or any available software
> that detect oligos with high frequency in given DNA sequence.
> I need to know the programs that detect any repeats without having the
> repeat characters through impute or database.
> I am trying to gather the software that excute this job.
> A.F.

Sequence landscapes might be appropriate for your problem.
The idea is that the program creates a list of all oligos
in a sequence or in a database, and then runs along
a test sequence, comparing each oligo in the test
sequence with the table. "Unusually long repeated sequences
show up as peaks on the landscape, and unusually rare
ones are seen as valleys".

Sequence Landscape, (1986) B. Cliff, D. Haussier, R. McConnell,
T. D. Schneider and G. D. Stormo, Nucleic Acids Research, 14: 141-158.

Levy S, Compagnoni L, Myers EW and Stormo G.D. (1998)
Xlandscape: The graphical display of word frequencies in
sequences. Bioinformatics 14:74-80. 

Xland for Unix/X windows is available by anonymous FTP at
beagle.colorado.edu in the directory pub/Landscape

Brian Fristensky                | 
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