Research Catalog

Title

Protein bioinformatics : an algorithmic approach to sequence and structure analysis / Ingvar Eidhammer and Inge Jonassen, William R. Taylor.

Author

Eidhammer, Ingvar.

Publication

Chichester, West Sussex, England ; Hoboken, NJ : J. Wiley & Sons, ©2004.

Items in the Library & Off-site

Details

Additional Authors

• Jonassen, Inge.
• Taylor, W. R. (Willie R.)

Description

xviii, 355 pages : illustrations; 24 cm

Summary

Takes the novel approach to cover both the sequence and structure analysis of proteins in one volume and from an algorithmic perspective. It provides a comprehensive introduction to the analysis of protein sequence and structure analysis; takes an algorithmic approach, relying on computational methods rather than theoretical; provides an integrated presentation of theory, examples, exercises and applications; and includes coverage of both protein structure, and sequence, analysis. This book is accessible enough for biologists, yet rigorous enough for computer scientists and mathematicians.

Alternative Title

Algorithmic approach to sequence and structure analysis

Subject

• Proteins > Structure
• Bioinformatics
• Proteins > Conformation
• Computational biology
• Algorithms
• Computer algorithms
• Protein Conformation
• Sequence Analysis, Protein
• Algorithms
• Computational Biology > methods
• Computational Biology
• algorithms
• Proteins > Conformation
• Computer algorithms
• Computational biology
• Bioinformatics
• Proteins > Structure
• Molekulare Bioinformatik
• Proteine
• Molekularbiologie

Bibliography (note)

• Includes bibliographical references (p. [337]-348) and index.

Contents

Sequence Analysis -- Pairwise Global Alignment of Sequences -- Alignment and Evolution -- A Scoring Scheme for the Model -- Finding Highest-Scoring Alignments with Dynamic Programming -- Determine H[subscript i, j] -- Use of matrices -- Finding the alignments that give the highest score -- Gaps -- Scoring Matrices -- Scoring Gaps: Gap Penalties -- Dynamic Programming for General Gap Penalty -- Dynamic Programming for Affine Gap Penalty -- Alignment Score and Sequence Distance -- Pairwise Local Alignment and Database Search -- The Basic Operation: Comparing Two Sequences -- Dot Matrices -- Filtering -- Repeating segments -- Dynamic Programming -- Initialization -- Finding the best local alignments -- Algorithms -- Scoring matrices and gap penalties -- Database Search: BLAST -- The procedure -- Preprocess the query: make the word list -- Scanning the database sequences -- Extending to HSP -- Introducing gaps -- Algorithm -- Statistical Analysis -- Hypothesis Testing for Sequence Homology -- Random generation of sequences -- Use of Z values for estimating the statistical significance -- Statistical Distributions -- Poisson probability distribution -- Extreme value distributions -- Theoretical Analysis of Statistical Significance -- The P value has an extreme value distribution -- Theoretical analysis for database search -- Probability Distributions for Gapped Alignments -- Assessing and Comparing Programs for Database Search -- Sensitivity and specificity -- Discrimination power -- Using more sequences as queries.

ISBN

• 9780470848395
• 0470848391

LCCN

2004299190

OCLC

• ocm54982066
• 54982066
• SCSB-1331551

Owning Institutions

Princeton University Library