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Bioinformatics of Genome Regulation and Structure

  • Book
  • © 2004

Overview

Editors:
  1. Nikolay Kolchanov

    1. Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia

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    You can also search for this editor in PubMed   Google Scholar

  2. Ralf Hofestaedt

    1. Bielefeld University, Bielefeld, Germany

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    You can also search for this editor in PubMed   Google Scholar

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Table of contents (35 chapters)

  1. Front Matter

    Pages I-XV
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  2. Computational Genomics

    1. Front Matter

      Pages 1-1
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    2. Nucleosomal DNA Organization: An Integrated Information System

      • V. G. Levitsky, A. V. Katokhin, O. A. Podkolodnaya, D. P. Furman
      Pages 3-12

    3. Using Change in Local DNA Sequence Complexity as a Pointer to the Mechanism of Mutagenesis in Inherited Disease

      • N. A. Chuzhanova, D. N. Cooper
      Pages 13-20

    4. Properties of Insertion Regions of Drosophila LTR Retrotransposons

      • D. P. Furman, D. Yu. Oshchepkov, M. A. Pozdnyakov, A. V. Katokhin
      Pages 21-31

    5. Compositional Asymmetries and Predicted Origins of Replication of the Saccharomyces Cerevisiae Genome

      • J. O. Korbel, H. E. Assmus, S. M. Kielbasa, H. Herzel
      Pages 33-38

    6. Revealing and Functional Analysis of Trna-Like Sequences in Various Genomes

      • F. E. Frenkel, M. B. Chaley, E. V. Korotkov, K. G. Skryabin
      Pages 39-46

    7. Type-Specific Features of the Structure of the tRNA Gene Promoters

      • Yu. V. Kondrakhin, I. B. Rogozin, T. M. Naykova, N. S. Yudin, M. I. Voevoda, A. G. Romashchenko
      Pages 47-60

    8. Mathematical Tools for Regulatory Signals Extraction

      • M. Régnier
      Pages 61-69

    9. Argo_Viewer: A Package for Recognition and Analysis of Regulatory Elements in Eukaryotic Genes

      • O. V. Vishnevsky, E. A. Ananko, E. V. Ignatieva, O. A. Podkolodnaya, I. L. Stepanenko
      Pages 71-80

    10. Transcription Regulatory Regions Database (TRRD): Description of Transcription Regulation and the Main Capabilities of the Database

      • E. V. Ignatieva, E. A. Ananko, O. A. Podkolodnaya, I. L. Stepanenko, T. M. Khlebodarova, T. I. Merkulova et al.
      Pages 81-91

    11. Sitecon—A Tool for Analysis of DNA Physicochemical and Conformational Properties: E2F/DP Transcription Factor Binding Site Analysis and Recognition

      • D. Yu. Oshchepkov, I. I. Turnaev, M. A. Pozdnyakov, L. Milanesi, E. E. Vityaev, N. A. Kolchanov
      Pages 93-102

    12. Local Secondary Structure May Be a Critical Characteristic Influencing Translation of Unicellular Organisms mRNA

      • Yu. G. Matushkin, V. A. Likhoshvai, A. V. Kochetov
      Pages 103-114

    13. Computer Analysis of miRNA-mRNA Duplexes and Its Application to Predicting Possible Target mRNAS of Arabidopsis

      • N. A. Omelyanchuk, D. G. Vorobiev
      Pages 115-124

    14. Correlations between Sequence Features of Yeast Genes Functional Regions and the Level of Expression

      • A. G. Pichueva, A. V. Kochetov, L. Milanesi, Yu. V. Kondrakhin, N. A. Kolchanov
      Pages 125-132

  3. Computational Structural Biology

    1. Front Matter

      Pages 133-133
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    2. Latent Periodicity of Many Domains in Protein Sequences Reflects Their Structure, Function, and Evolution

      • A. A. Laskin, E. V. Korotkov, N. A. Kudryashov
      Pages 135-143

    3. Logical Analysis of Data as a Predictor of Protein Secondary Structures

      • J. Błażewicz, P. L. Hammer, P. Łukasiak
      Pages 145-154

    4. Structure-Specificity Relationship in Protein-DNA Recognition

      • H. Kono, A. Sarai
      Pages 155-161

    5. Macromolecular Modeling as a Tool for Expanding Bioinformatics Databases

      • Yu. N. Vorobjev
      Pages 163-170
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Keywords

About this book

Bioinformatics of Genome Regulation and Structure covers:

-regulatory genomic sequences: databases, knowledge bases, computer analysis, modeling, and recognition;
-large-scale genome analysis and functional annotation;
-gene structure detection and prediction;
-comparative and evolutionary genomics;
-computer analysis of genome polymorphism and evolution; computer analysis and modeling of transcription, splicing, and translation; structural computational biology: structure-function organization of genomic DNA, RNA, and proteins;
-gene networks, signal transduction pathways, and genetically controlled metabolic pathways: principles of organization, operation, and evolution;
-data warehousing, knowledge discovery and data mining; and,
-analysis of basic patterns of genome operation, organization, and evolution.

The data presented may be used while solving a wide range of problems, both basic and applied, in various directions of molecular biology, molecular genetics, biotechnology, pharmacogenetics, pharmacology, and adjacent fields of medicine, veterinary, and agrobiology.

Editors and Affiliations

  • Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia

    Nikolay Kolchanov

  • Bielefeld University, Bielefeld, Germany

    Ralf Hofestaedt

Bibliographic Information

  • Book Title: Bioinformatics of Genome Regulation and Structure

  • Editors: Nikolay Kolchanov, Ralf Hofestaedt

  • DOI: https://doi.org/10.1007/978-1-4419-7152-4

  • Publisher: Springer New York, NY

  • eBook Packages: Springer Book Archive

  • Copyright Information: Springer Science+Business Media New York 2004

  • Hardcover ISBN: 978-1-4020-7735-7Published: 31 January 2004

  • Softcover ISBN: 978-1-4757-4613-6Published: 26 March 2013

  • eBook ISBN: 978-1-4419-7152-4Published: 05 June 2013

  • Edition Number: 1

  • Number of Pages: XVI, 374

  • Topics: Biochemistry, general, Evolutionary Biology, Animal Anatomy / Morphology / Histology

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