The storage, processing, description, transmission, connection, and analysis of the waves of new genomic data have made bioinformatics skills essential forscientists 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 strengthsand 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 servesmolecular biologists, geneticists, and biochemists as an enriched task-oriented manual, offering step-by-step guidance for the analysis of DNA sequences ina simple but meaningful fashion. Provides practical guidance and troubleshooting advice for the computational analysis of DNA sequences Covers a wide rangeof methods that unveil the multitude of applications and relevance of bioinformatics today Includes worked examples with real data that will direct the reader in completing specific bionformatic analyses Does not require a special background in statistics, mathematics or computer science, only a basic knowledge of molecular biology and genetics Describes only tools which are free and can be downloaded or accessed through the web Most chapters could be used for practical advanced undergraduate or graduate-level courses in bioinformatics andmolecular evolution INDICE: 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 PhylogeneticSupertrees Using Clann.- Detecting Signatures of Selection from DNA SequencesUsing 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 Mitochondria 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 usingSNPServer, dbSNP and SSR Taxonomy Tree.- Analysis of Transposable Element Sequences Using CENSOR and RepeatMasker.- DNA Sequence Polymorphism Analysis Using DnaSP.
- ISBN: 978-1-58829-910-9
- Editorial: Humana
- Encuadernacion: Cartoné
- Páginas: 340
- Fecha Publicación: 01/06/2009
- Nº Volúmenes: 1
- Idioma: Inglés