Publications on the methods and applications:
Prediction of functional sites in DNA sequences
by Variable Memory Markov models (context tree):
Orlov Yu.L., Potapov V.N., Filippov V.P. (2002)
Recognizing functional DNA sites and segmenting genomes
using the program "Complexity"
// Proceedings of the Third International Conference on Bioinformatics of
Genome Regulation and Structure (BGRS'2002), Novosibirsk, Institute of Cytology&Genetics
Press, Vol.3, p.244-247.
Orlov
Yu.L.,
Filippov V.P., Potapov V.N., Kolchanov N.A. (2002) Construction of stochastic
context trees for genetic texts. In Silico Biology, (IOS Press) 2(3), 233-247.
Nucleosome
formation site analysis:
Levitsky
V.G., Podkolodnaya O.A., Kolchanov N.A., Podkolodny N.L. (2001) Nucleosome
formation potential of exons, introns, and Alu repeats. Bioinformatics 17(11):
1062-4.
Orlov
Yu.L., Levitsky V.G. (2004)
Nucleosome
positioning signal analysis. // Proceedings of BGRS'2004, Novosibirsk, Inst. of
Cytology&Genetics Press, Vol.1, p.149-152.
Levitsky
V.G., Proscura A.P., Podkolodnaya O.A., Ignatieva E.V., Ananko E.A. (2004)
Nucleosome
formation potential of the gene regulatory regions.
Proceedings of the Fourth International Conference on
Bioinformatics of
Genome Regulation and
Structure (BGRS'2004), IC&G
Press, Novosibirsk, Vol.1,
p.130-133.
Programs:
Levitsky
V.G., Podkolodnaya O.A., Kolchanov N.A., Podkolodny N.L. (2001) Nucleosome
formation potential of eukaryotic DNA: tools for calculation and promoters
analysis. Bioinformatics, 17(11), 998–1010.
Levitsky
V.G. (2004) RECON: a program for prediction of nucleosome formation potential. Nucleic
Acids Res. 32(Web Server issue):W346-9.
Database:
Levitsky
VG, Ponomarenko MP, Ponomarenko JV, Frolov AS, Kolchanov NA. (1999) Nucleosomal
DNA property database. Bioinformatics 15(7-8):582-92.
Levitsky
V.G., Katokhin A.V., Podkolodnaya O.A., Furman D.P., Kolchanov N.A. (2005) NPRD:
Nucleosome Positioning Region Database. Nucleic Acids Res. 33 Database
Issue:D67-70.
Additional materials including complete Proceedings of the BGRS conferences
(2000, 2002 and 2004) in PDF format are accessible at the official Internet-site
of the series of International
Conferences on Bioinformatics of Genome Regulation and Structure.
Main page
This resource has been developed in Institute of Cytology
and Genetics, Novosibirsk, Russia
Authors: Yu.L.Orlov,
V.G.Levitsky
Leader: N.A.Kolchanov
Version - 2005.