Bioinformatics and Computational Biology Solutions Using R and Bioconductor

"This book is more than a static collection of descriptive text, figures, and code examples that were run by the authors to produce the text; it is a dynamic document. Code underlying all of the computations that are shown is made available on a companion website, and readers can reproduce every number, figure, and table on their own computers."--Jacket. Sequence databases / Rolf Apweiler -- Mapping databases / Tara Matise and Peter S. White -- Information retrieval from biological databases / Andreas D. Baxevanis -- Genomic databases / Tyra Wolfsberg -- Predictive methods using DNA sequences / Roderic Guigó and Enrique Blanco -- Predictive methods using RNA sequences / Michael Zucker and David Mathews -- Sequence polymorphisms / James C. Mullikin and Stephen T. Sherry -- Predictive methods using protein sequences / Burkhard Rost and Yanay Ofran -- Protein structure prediction and analysis / David Wishart -- Intermolecular interactions and biological pathways / Gary D. Bader and Anton J. Enright -- Assessing pairwise sequence similarity: blast and fasta / Andreas D. Baxevanis -- Creation and analysis of protein multiple sequence alignments / Geoffrey J. Barton -- Sequence assembly and finishing methods / Gerard Bouffard, Nancy F. Hansen, and Pamela Jacques Thomas -- Phylogenetic analysis / Fiona S.L. Brinkman -- Computational approaches in comparative genomics / Andreas D. Baxevanis -- Microarray analysis / John Quackenbush -- Proteomics and protein identification / Michael Giddings, Mark R. Holmes, and Kevin Ramkissoon -- Using perl to facilitate biological analysis / Lincoln D. Stein