Bioinformatics for DNA Sequence Analysis / Edition 1

by David Posada

Overview

The recent accumulation of information from genomes, including their sequences, has resulted not only in new attempts to answer old questions and solve longstanding issues in biology, but also in the formulation of novel hypotheses that a rise precisely from this wealth of data. The storage, processing, description, transmission, connection, and analysis of these data has prompted bioinformatics to become one the most relevant applied sciences for this new century, walking hand-in-hand with modern molecular biology and clearly impacting areas like biotechnology and biomedicine. Bioinformatics skills have now become essential for many scientists working with DNA sequences. With this idea in mind, this book aims to provide practical guidance and troubleshooting advice for the computation alanalysis of DNA sequences, covering a range of issues and methods that unveil the multitude of applications and relevance that Bioinformatics has today. The analysis of protein sequences has been purposely excluded to gain focus. Individual book chapters are oriented toward the description of the use of specific bioinformatics tools, accompanied by practical examples, a discussion on the interpretation of results, and specific comments on strengths and limitations of the methods and tools. In a sense, chapters could be seen as enriched task-oriented manuals that will direct the reader in completing specific bioinformatics analyses. The target audience for this book is biochemists, and molecular and evolutionary biologists that want to learn how to analyze DNA sequences in asimple but meaningful fashion. Readers do not need a special background in statistics, mathematics, or computer science, just a basic knowledge of molecular biology and genetics. All the tools described in the book are free and all of them can be downloaded or accessed through the web. Most chapters could be used for practical advanced under graduate or graduate-level courses in bioinformatics and molecular evolution.

Product Details

ISBN-13:	9781617378393
Publisher:	Springer-Verlag New York, LLC
Publication date:	11/19/2010
Series:	Methods in Molecular Biology , #537
Edition description:	Softcover reprint of hardcover 1st ed. 2009
Pages:	354
Product dimensions:	7.60(w) x 10.24(h) x 0.03(d)

Table of Contents

Similarity Searching Using BLAST.- Gene Orthology Assessment with OrthologID.- Multiple Alignment of DNA Sequences with MAFFT.- SeqVis: A Tool for Detecting Compositional Heterogeneity Among Aligned Nucleotide Sequences.- Selection of Models of DNA Evolution with jModelTest.- Estimating Maximum Likelihood Phylogenies with PhyML.- Trees from Trees: Construction of Phylogenetic Supertrees Using Clann.- Detecting Signatures of Selection from DNA Sequences Using Datamonkey.- Recombination Detection and Analysis Using RDP3.- CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition.- Genetic Code Prediction for Metazoan Mihondria with GenDecoder.- Computational Gene Annotation in New Genome Assemblies Using GeneID.- Promoter Analysis: Gene Regulatory Motif Identification with A-GLAM.- Analysis of Genomic DNA with the UCSC Genome Browser.- Mining for SNPs and SSRs Using SNPServer, dbSNP and SSR Taxonomy Tree.- Analysis of Transposable Element Sequences Using CENSOR and RepeatMasker.- DNA Sequence Polymorphism Analysis Using DnaSP.