Handbook of Hidden Markov Models in Bioinformatics

Handbook of Hidden Markov Models in Bioinformatics

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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.show more

Product details

  • Hardback | 176 pages
  • 157.48 x 236.22 x 17.78mm | 408.23g
  • Taylor & Francis Inc
  • Chapman & Hall/CRC
  • Boca Raton, FL, United States
  • English
  • 57 black & white illustrations, 2 black & white tables, 1 black & white halftones
  • 1584886846
  • 9781584886846

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.show more