Bioinformatics of Genome Regulation and Structure II

Computational Structural, Functional and Evolutionary Genomics

1. Front Matter

   Pages 1-1

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2. Recognition of Coding Regions in Genome Alignment

   • T. V. Astakhova, S. V. Petrova, I. I. Tsitovich, M. A. Roytberg

   Pages 3-10

3. Predicting sRNA Genes in the Genome of E. Coli by the Promoter-Search Algorithm PlatProm

   • A. S. Brok-Volchanski, I. S. Masulis, K. S. Shavkunov, V. I. Lukyanov, Yu. A. Purtov, E. G. Kostyanicina et al.

   Pages 11-20

4. Content Sensors Based on Codon Structure and DNA Methylation for Gene Finding in Vertebrate Genomes

   • X. Xia

   Pages 21-29

5. The Sitega Tool for Recognition and Context Analysis of Transcription Factor Binding Sites: Significant Dinucleotide Features Besides the Canonical Consensus Exemplified By SF-1 Binding Site

   • V. Levitsky, E. Ignatieva, G. Vasiliev, N. Limova, T. Busygina, T. Merkulova et al.

   Pages 31-41

6. Transcription Regulatory Regions Database (TRRD): A Source of Experimentally Confirmed Data on Transcription Regulatory Regions of Eukaryotic Genes

   • N. Kolchanov, E. Ignatieva, O. Podkolodnaya, E. Ananko, I. Stepanenko, T. Merkulova et al.

   Pages 43-53

7. Artsite Database: Comparison of In Vitro Selected and Natural Binding Sites of Eukaryotic Transcription Factors

   • T. Khlebodarova, O. Podkolodnaya, D. Oshchepkov, D. Miginsky, E. Ananko, E. Ignatieva

   Pages 55-65

8. Comparative Analysis of Electrostatic Patterns for Promoter and Nonpromoter DNA in E. Coli Genome

   • S. G. Kamzolova, A. A. Sorokin, P. M. Beskaravainy, A. A. Osypov

   Pages 67-74

9. Analysis of Nucleosome Formation Potential and Conformational Properties of Human J1-J2 and D2-D1 Type Alpha Satellite DNA

   • A. Katokhin, V. Levitsky, D. Oshchepkov, A. Poplavsky, V. Trifonov, D. Furman

   Pages 75-83

10. VMM: A Variable Memory Markov Model Prediction of Nucleosome Formation Sites

    • Yu. L. Orlov, V. G. Levitsky, O. G. Smirnova, O. A. Podkolodnaya, T. M. Khlebodarova, N. A. Kolchanov

    Pages 85-95

11. DNA Nucleosome Organization of the Promoter Gene Regions

    • V. G. Levitsky, A. G. Pichueva, A. V. Kochetov, L. Milanesi

    Pages 97-103

12. A Toolbox for Analysis of RNA Secondary Structure Based on Genetic Algorithm

    • I. Titov, D. Vorobiev, A. Palyanov

    Pages 105-110

13. Comparative Genomics and Evolution of Bacterial Regulatory Systems

    • M. S. Gelfand, A. V. Gerasimova, E. A. Kotelnikova, O. N. Laikova, V. Y. Makeev, A. A. Mironov et al.

    Pages 111-119

14. Comparative Whole Genome Sequence Analysis of Corynebacteria

    • Y. Nishio, Y. Usuda, T. Gojobori, K. Ikeo

    Pages 121-129

15. New LTR Retrotransposable Elements from Eukaryotic Genomes

    • O. Novikova, M. Fursov, E. Beresikov, A. Blinov

    Pages 131-140

16. A Genome-Wide Identification of Mitochondrial DNA Topoisomerase I in Arabidopsis

    • A. Katyshev, I.B. Rogozin, Yu. Konstantinov

    Pages 141-145

17. Change in CpG Context is a Leading Cause of Correlation between the Rates of Non-Synonymous and Synonymous Substitutions in Rodents

    • G. Bazykin, A. Ogurtsov, A. Kondrashov

    Pages 147-151

18. Universal Seven-Cluster Structure of Genome Fragment Distribution: Basic Symmetry in Triplet Frequencies

    • A. Gorban, A. Zinovyev, T. Popova

    Pages 153-163

19. New Methods to Infer DNA Function from Sequence Information

    • I. Abnizova, R. te Boekhorst, K. Walter, W. R. Gilks

    Pages 165-177