Return to the main menu Help Publications Results Related program: RECON Nucleosome database
Here is an example of VMM program. The sequence contains nucleosome formation site with flanks,
total length is 400 bp. Press Execute button to see text profile output.
The output in text format looks like tab-delimited columns of digits:
Make profile for whole sequence
--- Seq.num.1, length 1100 bp
Probability for window 50 bp
Position shift 0 bp
. . .
To change sliding window size or profile step you can input appropriate integer value in the fields above.
The program allows usage of pre-calculated model for a set of DNA sequences. Please construct such model by the related program: Complexity by context tree source
Output of this program (oligonucleotides and frequencies in text file) could be used as a VMM model for prediction (cut and paste in the form). Option "user-defined model" should be selected in the appropriate drop-down menu instead of "Nucleosome formation sites". We have some variants of training sample containing nucleosome formation sites: sequences of 146 bp length and sequences 120 bp length phased relative to the site center.
Graphic mode option show standard profile visualization plot instead of the text output. The graphic profile corresponds to whole sequence in the case of 'Single sequence' options selected or an averaged profile if one of 'Set of phased sequence' options was selected.
Authors: Yu.L.Orlov, V.G.Levitsky
S.V.Lavryushev, D.A.Grigorovich, S.A.Poplavsky
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