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Modern Genome Annotation

The Biosapiens Network

  • Book
  • © 2008

Overview

Editors:
  1. Dmitrij Frishman

    1. Wissenschaftszentrum Weihenstephan, TU München, Freising, Germany

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    You can also search for this editor in PubMed   Google Scholar

  2. Alfonso Valencia

    1. Structural and Computational Programme, Spanish National Cancer Research Centre, Madrid, Spain

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Cutting-edge genome analysis methods from leading bioinformaticians

  • Includes supplementary material: sn.pub/extras

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Table of contents (20 chapters)

  1. Front Matter

    Pages I-XVIII
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  2. Introduction BIOSAPIENS: A European Network of Excellence to develop genome annotation resources

    1. Introduction BIOSAPIENS: A European Network of Excellence to develop genome annotation resources

      • Dmitrij Frishman, Alfonso Valencia
      Pages 1-3

  3. Gene definition

    1. Front Matter

      Pages 5-5
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    2. State of the art in eukaryotic gene prediction

      • T. Alioto, R. Guigó
      Pages 7-39

    3. Quality control of gene predictions

      • A. Nagy, H. Hegyi, K. Farkas, H. Tordai, E. Kozma, L. Bányai et al.
      Pages 41-52

  4. Gene regulation and expression

    1. Front Matter

      Pages 53-53
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    2. Evaluating the prediction of cis-acting regulatory elements in genome sequences

      • O. Sand, J.-V. Turatsinze, J. van Helden
      Pages 55-89

    3. A biophysical approach to large-scale protein-DNA binding data

      • T. Manke, H. Roider, M. Vingron
      Pages 91-103

    4. From gene expression profiling to gene regulation

      • R. Coulson, T. Manke, K. Palin, H. Roider, O. Sand, J. van Helden et al.
      Pages 105-119

  5. Annotation and genetics

    1. Front Matter

      Pages 121-121
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    2. Annotation, genetics and transcriptomics

      • R. Mott
      Pages 123-136

  6. Functional annotation of proteins

    1. Front Matter

      Pages 137-137
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    2. Resources for functional annotation

      • A. J. Bridge, A.-Lise Veuthey, N. J. Mulder
      Pages 139-164

    3. Annotating bacterial genomes

      • C. Médigue, A. Danchin
      Pages 165-190

    4. Data mining in genome annotation

      • I. Artamonova, S. Kramer, D. Frishman
      Pages 191-212

    5. Modern genome annotation: the BioSapiens network

      • C. Yeats, Ch. Orengo, A. Lise Veuthey, B. Boeckmann, L. Juhl Jensen, A. Valencia et al.
      Pages 213-238

    6. Structure to function

      • J. D. Watson, J. M. Thornton, M. L. Tress, G. Lopez, A. Valencia, O. Redfern et al.
      Pages 239-262

    7. Harvesting the information from a family of proteins

      • B. Vroling, G. Vriend
      Pages 263-279

  7. Protein structure prediction

    1. Front Matter

      Pages 281-281
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    2. Structure prediction of globular proteins

      • A. Tramontano, D. Jones, L. Rychlewski, R. Casadio, P. Martelli, D. Raimondo et al.
      Pages 283-307
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Keywords

About this book

An accurate description of current scientific developments in the field of bioinformatics and computational implementation is presented by research of the BioSapiens Network of Excellence. Bioinformatics is essential for annotating the structure and function of genes, proteins and the analysis of complete genomes and to molecular biology and biochemistry.

Included is an overview of bioinformatics, the full spectrum of genome annotation approaches including; genome analysis and gene prediction, gene regulation analysis and expression, genome variation and QTL analysis, large scale protein annotation of function and structure, annotation and prediction of protein interactions, and the organization and annotation of molecular networks and biochemical pathways. Also covered is a technical framework to organize and represent genome data using the DAS technology and work in the annotation of two large genomic sets: HIV/HCV viral genomes and splicing alternatives potentially encoded in 1% of the human genome.

Editors and Affiliations

  • Wissenschaftszentrum Weihenstephan, TU München, Freising, Germany

    Dmitrij Frishman

  • Structural and Computational Programme, Spanish National Cancer Research Centre, Madrid, Spain

    Alfonso Valencia

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