Handbook of Hidden Markov Models in Bioinformatics

Series:
Chapman & Hall/CRC Mathematical & Computational Biology
Published:
June 12, 2008 by Chapman and Hall/CRC - 176 Pages
Author(s):
Martin Gollery, Tahoe Informatics, Incline Village, Nevada, USA

Purchasing Options

Hardback
$67.95
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ISBN 9781584886846
Cat# C6846
 

Features

  • Explores HMM implementations important in bioinformatics, including SAM, HMMER, Wise2, PSI-BLAST, and Meta-MEME
  • Shows how numerous databases and programs, such as Pfam, SMART, SUPERFAMILY, and PANTHER, are used in bioinformatics projects
  • Focuses on the use of HMMs for discovering the homology of a protein family
  • Explains how to build custom HMM databases
  • Offers solutions to help overcome slow searches
  • Provides problem sets at the end of each chapter to encourage further study
  • Includes a CD-ROM with related material and programs

    • Summary

    Demonstrating that many useful resources, such as databases, can benefit most bioinformatics projects, the Handbook of Hidden Markov Models in Bioinformatics focuses on how to choose and use various methods and programs available for hidden Markov models (HMMs).

    The book begins with discussions on key HMM and related profile methods, including the HMMER package, the sequence analysis method (SAM), and the PSI-BLAST algorithm. It then provides detailed information about various types of publicly available HMM databases, such as Pfam, PANTHER, COG, and metaSHARK. After outlining ways to develop and use an automated bioinformatics workflow, the author describes how to make custom HMM databases using HMMER, SAM, and PSI-BLAST. He also helps you select the right program to speed up searches. The final chapter explores several applications of HMM methods, including predictions of subcellular localization, posttranslational modification, and binding site.

    By learning how to effectively use the databases and methods presented in this handbook, you will be able to efficiently identify features of biological interest in your data.

    Table of Contents

    Introduction to HMMs and Related Profile Methods
    Introduction to Sequence Analysis
    Pairwise Algorithms: Smith–Waterman, FASTA, and BLAST
    Pairwise Limitations
    The Advantages of Profile Methods
    The Rise of Profile HMMs
    Regular Expressions
    But What Exactly Is an HMM?
    Curated vs. Noncurated Databases
    Disadvantages and Limitations of Profile HMMs for Bioinformatics
    Profile HMMs
    A General Model HMMs
    Plan 7 from Janelia Farms
    Local Scoring
    Global Alignments
    The Maximum Entropy Model
    Statistics
    Other Uses for HMMs in Biology
    HMM Methods
    The HMMER Suite of Programs
    Creating Multiple Alignments with HMMs
    SAM
    PSI-BLAST, PSI-TBLASTN, and RPS-BLAST
    Regular Expression Methods
    MEME and Meta-MEME
    Wise2
    Commercial and Alternative HMM Implementations
    HMMER Options
    HMM Databases
    The Many Flavors of Pfam
    SMART
    TIGRfam
    SUPERFAMILY
    PANTHER
    PRED-GPCR
    CDD
    COG
    The TLfam Database
    KINfam
    PRIAM and metaSHARK
    NODE
    FPfam
    KinasePhos
    Building an Analytical Pipeline
    What Is an Analytical Pipeline?
    How Do I Create a Pipeline and What Do I Put Into It?
    Is There An Easier Way to Manage My Workflow?
    Are There Any Pipelines That I Can Simply Download and Install?
    Building Custom Databases
    Building HMMER Databases
    Building Databases with the SAM Package
    Building PSSM Databases for RPS-BLAST
    Building Regular Expression Databases
    Speeding Your Searches
    Pick Your Targets Carefully
    Format Selection
    Optimized Solutions
    Accelerated Computing
    GeneWise
    Other Uses of HMMs in Bioinformatics
    Methods Comparing HMMs to Other HMMs
    Subcellular Localization Prediction
    Posttranslational Modification Prediction
    Binding Site Predictions
    Gene Finding Programs
    MEME, MAST, and Meta-MEME
    Index
    An Introduction, a Summary, and Questions appear in each chapter.

    Editorial Reviews

    "…a book on how to use software packages based on HMMs for the purpose of doing bioinformatics analyses and database searches. The book’s audience is those who want to use the tools … ."
    —Biometrics, December 2008

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