Bioinformatics for DNA sequence analysis / edited by David Posada.

Includes bibliographical references and index.

Similarity searching using BLAST / Kit J. Menlove, Mark Clement, and Keith A. Crandall -- Gene orthology assessment with OrthologID / Mary Egan ... [et al.] -- Multiple alignment of DNA sequences with MAFFT / Kazutaka Katoh, George Asimenos, and Hiroyuki Toh -- SeqVis : a tool for detecting compositional heterogeneity among aligned nucleotide sequences / Lars Sommer Jermiin ... [et al.] -- Selection of models of DNA evolution with jModelTest / David Posada -- Estimating maximum likelihood phylogenies with PhyML / Stéphane Guindon ... [et al.] -- Trees from trees : construction of phylogenetic supertrees using clann / Christopher J. Creevey and James O. McInerney -- Detecting signatures of selection from DNA sequences using datamonkey / Art F.Y. Poon, Simon D.W. Frost, and Sergei L. Kosakovsky Pond -- Recombination detection and analysis using RDP3 / Darren P. Martin -- CodonExplorer : an interactive online database for the analysis of codon usage and sequence composition / Jesse Zaneveld ... [et al.] -- Genetic code prediction for metazoan mitochondria with GenDecoder / Federico Abascal, Rafael Zardoya, and David Posada -- Computational gene annotation in new genome assemblies using GeneID / Enrique Blanco and Josep F. Abril -- Promoter analysis : gene regulatory motif identification with A-GLAM / Leonardo Mariño-Ramírez ... [et al.] -- Analysis of genomic DNA with the UCSC Genome Browser / Jonathan Pevsner -- Mining for SNPs and SSRs using SNPServer, dbSNP and SSR taxonomy tree / Jacqueline Batley and David Edwards -- Analysis of transposable element sequences using CENSOR and RepeatMasker / Ahsan Huda and I. King Jordan -- DNA sequence polymorphism analysis using DnaSP / Julio Rozas.

The storage, processing, description, transmission, connection, and analysis of the waves of new genomic data have made bioinformatics skills essential for scientists working with DNA sequences. In Bioinformatics for DNA Sequence Analysis, experts in the field provide practical guidance and troubleshooting advice for the computational analysis of DNA sequences, covering a range of issues and methods that unveil the multitude of applications and the vital relevance that the use of bioinformatics has today. Individual book chapters explore the use of specific bioinformatic tools, accompanied by practical examples, a discussion on the interpretation of results, and specific comments on strengths and limitations of the methods and tools. As a part of the highly successful Methods in Molecular Biology series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Focused and cutting-edge, Bioinformatics for DNA Sequence Analysis serves molecular biologists, geneticists, and biochemists as an enriched task-oriented manual, offering step-by-step guidance for the analysis of DNA sequences in a simple but meaningful fashion.

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