Variable memory Markov (VMM) model 

for nucleosome formation site prediction

 

 

Example      Help      Publications     Results     Related program: RECON       Nucleosome database

  

Input sequence(s) here (FASTA format or plain text) (cut & paste)

or From file

Profile parameters:

Sliding window size, bp (>10)       Profile step (shift of sliding window)

   

use pre-defined VMM models (nucleosome):


or input pre-calculated VMM model in text format here (calculated by TreeComplexity program)  

(cut & paste)

or  from File:

 

Output details:   Single sequence

Prediction profile only         Detailed profile (position and logarithm probability)

 

Set of phased sequence (averaged profile) 

Mean profile only  

Detailed report (Mean, standard deviation + profiles for every seq. in the set)  

 

Supplementary output options:

Shift position (Profile 0 position)  bp

Centering position (Profile 0 position in the center of the sequence) Yes  No

 

                

Construction of VMM model for set of DNA sequences: Complexity by context tree source

The Institute of Cytology and Genetics (Russia)

Authors: Yu.L.Orlov, V.G.Levitsky
Contributors: S.V.Lavryushev, D.A.Grigorovich, S.A.Poplavsky
Leader: N.A.Kolchanov

The research was partially supported by the Russian Foundation for Basic Research (RFBR) and Siberian Branch of the Russian Academy of Sciences (Integration project No. 119).