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DNA Research Advance Access published online on September 16, 2006
DNA Research, doi:10.1093/dnares/dsl004
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© The Author 2006. Kazusa DNA Research Institute.
Received April 12, 2006
Revised June 1, 2006

Full Papers

Search and Classification of Potential Minisatellite Sequences from Bacterial Genomes

Konstantin Skryabin 1, Eugene Korotkov 1, and Andrew Shelenkov 1 *

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

* To whom correspondence should be addressed.
Andrew Shelenkov, E-mail: fallandar{at}mail.ru


  Abstract

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.

Keywords: information decomposition; modified profile analysis; minisatellites; bacterial genomes.
Communicated by Kenta Nakai
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