Bioinformatics Algorithms

This book introduces algorithmic techniques in bioinformatics, emphasizing their application to solving novel problems in post-genomic molecular biology. Beginning with a thought-provoking discussion on the role of algorithms in twenty-first-century bioinformatics education, Bioinformatics Algorithms covers:

• General algorithmic techniques, including dynamic programming, graph-theoretical methods, hidden Markov models, the fast Fourier transform, seeding, and approximation algorithms

• Algorithms and tools for genome and sequence analysis, including formal and approximate models for gene clusters, advanced algorithms for non-overlapping local alignments and genome tilings, multiplex PCR primer set selection, and sequence/network motif finding

• Microarray design and analysis, including algorithms for microarray physical design, missing value imputation, and meta-analysis of gene expression data

• Algorithmic issues arising in the analysis of genetic variation across human population, including computational inference of haplotypes from genotype data and disease association search in case/control epidemiologic studies

• Algorithmic approaches in structural and systems biology, including topological and structural classification in biochemistry, and prediction of protein-protein and domain-domain interactions

Each chapter begins with a self-contained introduction to a computational problem; continues with a brief review of the existing literature on the subject and an in-depth description of recent algorithmic and methodological developments; and concludes with a brief experimental study and a discussion of open research challenges. This clear and approachable presentation makes the book appropriate for researchers, practitioners, and graduate students alike.