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oligo frequency

Ahmed Fadiel afadiel at bioinfo.sickkids.on.ca
Thu May 18 14:37:25 EST 2000


This was really helpful.
Thanks a lot.
Ahmed

Brian Fristensky wrote:

> 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
>
> --
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