Example. Variable memory Markov (VMM) model

for nucleosome formation site prediction

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
25 -56.403
35 -57.878
45 -57.827
55 -57.556
65 -58.841
75 -59.014
85 -58.508
95 -58.570
105 -58.323
. . .

Input sequence(s) here (FASTA format or plain text) (cut & paste)
>P00038 ttcactcttgaagccagcaaggccatgaacccaccaggaggaacaaacaactctggacgt gccatgtttaagagctgtaacactcactgtgaaggtctgcagcttcactcctgaagtcag tgagaccatgaagccactgggaggaatgaacaactctggacatgtcacctttaagagctc tgacactcactgcgaaggtctgcagcttctggacacaatactattcattctcaccttaaa gacgaggaaactaaggcaaagaacagtcaactaataagtccaagtatacagagctgctaa ggaatagtctgtctgatcccaaaggctgtgtcataaccgcttccctatactgcctctcag cagaggtaagagtcaagttttatttatcactgccaccccatcagccccagcttagtgcct gacacagggagatgctcaatcaatgctgattgttattgagtggactagaaatgcaaggca cagtgagcccctttgctgtgactgatggggtgtctgattttctgctataaagaggagagt gctgtatcaaacacactcctctggctcctagctctctctgttcactttgtttatccaatt tccctactcctccttcataactgcaccatgtggattcaaaattgcagcttagtgcagaca aagggaaaacggaattctgaatgaccccaaagggaaaactgaactctgaatgacccctgt gggtttgagagaagagaagcaggaacttgagagaggaggaagagagaaagtaattaaaat gtatcgttttaacttaatatttaaccgaatgatagcaaaatcttatctgaaattggaaaa gtcaaggttttgagtgctggttcggtgcccatttctttatgatttgatagtctgagaaga atacgacgggtgtggcttaaaaacctagatcacgtgtgtagttggaattgggtgttatat gagcaaacaaaataaatacctgtgcaacatacctgctttatgcactcaagcagagaagaa atccacaagtactcaccagcctcctggtctgcagagaagacagaatcaatatgagcacag caggaaaagtaagcaaaaaa >P00370 gacttctcgggctcaagcaatcctcccacctcagcctcccaagtagctgggactacgggc acacgccaccatgcctggctaatttttgtattttttgtagagatgggtcttcaccatgtt gatcaggctggtctcgaactcctgggctcatgcgatccaccccgccagctgattacaggg attccggtggtgagccaccgcgcccagacgccacttcatcgtattgtaaacgtctgttac ctttctgttcccctgtctactggactgtgagctccttagggccacgaattgaggatgggg cacagagcaagctctccaaacgtttgttgaatgagtgagggaatgaatgagttcaagcag atgctatacgttggctgttggagattttggctaaaatgggacttgcaggaaagcccgacg tccccctcgccatttccaggcaccgctcttcagcttgggctctgggtgagcgggataggg ctgggtgcaggattaggataatgtcatgggtgaggcaagttgaggatggaagaggtggct gatggctgggctgtggaactgatgatcctgaaaagaagaggggacagtctctggaaatct aagctgaggctgttgggggctacaggttgagggtcacgtgcagaagagaggctctgttct gaacctgcactatagaaaggtcagtgggatgcgggagcgtcggggcggggcggggcctat gttcccgtgtccccacgcctccagcaggggacgcccgggctgggggcggggagtcagacc gcgcctggtaccatccggacaaagcctgcgcgcgccccgccccgccattggccgtaccgc cccgcgccgccgccccatcccgcccctcgccgccgggtccggcgcgttaaagccaatagg aaccgccgccgttgttcccgtcacggccggggcagccaattgtggcggcgctcggcggct cgtggctctttcgcggcaaaaaggatttggcgcgtaaaagtggccgggactttgcaggca gcggcggccgggggcggagcgggatcgagccctcgccgaggcctgccgccatgggcccgc gccgccgccgccgcctgtca >P00371 gacttctcgggctcaagcaatcctcccacctcagcctcccaagtagctgggactacgggc acacgccaccatgcctggctaatttttgtattttttgtagagatgggtcttcaccatgtt gatcaggctggtctcgaactcctgggctcatgcgatccaccccgccagctgattacaggg attccggtggtgagccaccgcgcccagacgccacttcatcgtattgtaaacgtctgttac ctttctgttcccctgtctactggactgtgagctccttagggccacgaattgaggatgggg cacagagcaagctctccaaacgtttgttgaatgagtgagggaatgaatgagttcaagcag atgctatacgttggctgttggagattttggctaaaatgggacttgcaggaaagcccgacg tccccctcgccatttccaggcaccgctcttcagcttgggctctgggtgagcgggataggg ctgggtgcaggattaggataatgtcatgggtgaggcaagttgaggatggaagaggtggct gatggctgggctgtggaactgatgatcctgaaaagaagaggggacagtctctggaaatct aagctgaggctgttgggggctacaggttgagggtcacgtgcagaagagaggctctgttct gaacctgcactatagaaaggtcagtgggatgcgggagcgtcggggcggggcggggcctat gttcccgtgtccccacgcctccagcaggggacgcccgggctgggggcggggagtcagacc gcgcctggtaccatccggacaaagcctgcgcgcgccccgccccgccattggccgtaccgc cccgcgccgccgccccatcccgcccctcgccgccgggtccggcgcgttaaagccaatagg aaccgccgccgttgttcccgtcacggccggggcagccaattgtggcggcgctcggcggct cgtggctctttcgcggcaaaaaggatttggcgcgtaaaagtggccgggactttgcaggca gcggcggccgggggcggagcgggatcgagccctcgccgaggcctgccgccatgggcccgc gccgccgccgccgcctgtca >P00341 atctctgttgcttacatattttagaatgaatttcatttaggagtctaagtctactacgaa ggcactgccttatctaaatgtctctaaacatacctcctgcctatcacaaagacatagaat ctcactcacaagagtcaaagttgttcattccaccaggagagataaggctggaccaaaagc acccctgggtttaagtccacactccccaccaccccggcccccacccccaagcagtgacag actgtcttgaactctctcgctgcaagggtcataaaagggacagagaacagagcgacagaa gatgtcttctgcattctcaacttttagccccagttgttagagaactggtatctcccctac acgtctggctctggtggagaaagaatgacagcccctacttacaacgaggagactgtggct cagagaagttagggggctgcccaggatcctggagaaagccagctttgactcataaccctc gcgccattacctgactcccattagtggagtcaggaactccatgttccacttcaggaaatg agcttgttgatttttcatttacacaaaaatgaaaaataaataccacatgtttgaaaacat gttgcaacacgtcctgctggaacttaaaagtgcattctgaccaaaaaaattaaattagaa aatccacatagcaaaaaaaaaaatgttttggatgaaaatatactttatctttctctcaca catactctctctctctctcgcacacatacccacacacacacacacacacacacacacaca cacacgcgcgaaaacaatatctcatttcttcttcagggagcagctgtgaaggaaatcggg ggaggaggatggacacaacatcccatctttgtgtttcgatacagactaagcttttaggcc aaccctcctgactggatgggggcggcgggcgtggcatgcatgaaaagtaaacatcagaga cctgaagaagcttataaaatagcttgggagaggccagtcaccaagacaggcatctcaaat cggctgattctgcatctggaaactgccttcatcttgaaagaaaaggtatgtactgtagtt ttaagcttttcatttatgat

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

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

Contributors: S.V.Lavryushev, D.A.Grigorovich, S.A.Poplavsky
Leader: N.A.Kolchanov

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