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DNA Research Advance Access originally published online on September 16, 2006
DNA Research 2006 13(3):89-102; doi:10.1093/dnares/dsl004
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© The Author 2006. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Search and Classification of Potential Minisatellite Sequences from Bacterial Genomes

Andrew Shelenkov*, Konstantin Skryabin and Eugene Korotkov

Bioengineering Centre of Russian Academy of Sciences, Prospect 60-tya Oktyabrya 7/1, 117312 Moscow, Russia

We used the method of Information Decomposition developed by us to identify the latent dinucleotide periodicity regions in bacterial genomes. The number of potential minisatellite sequences obtained at high level of statistical significance was 454. Then we classified the periodicity matrices and obtained 45 classes. We used the other new method developed by us—Modified Profile Analysis—to reveal more periodic sequences in the presence of indels using the classes obtained. The number of sequences found by combination of these two methods was 3949. Most of them cannot be revealed by other methods including dynamic programming and Fourier transformation.

Key words: information decomposition; modified profile analysis; minisatellites; bacterial genomes

*To whom correspondence should be addressed. Tel. +7-495-135-2161. Fax +7-495-135-2161. E-mail: fallandar{at}mail.ru

Communicated by Kenta Nakai


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