Bioinformatics for DNA Sequence Analysis

ISBN-13: 9781588299109 / Angielski / Twarda / 2009 / 354 str.

David Posada

Opis

The recent accumulation of information from genomes, including their sequences, has resultednotonlyinnewattemptstoansweroldquestionsandsolvelongstandingissues inbiology, butalsointheformulationofnovelhypothesesthatarisepreciselyfromthis 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 andtroubleshootingadviceforthecomputationalanalysisofDNAsequences, 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 excludedtogainfocus.Individualbookchaptersareorientedtowardthedescriptionof theuseofspecificbioinformaticstools, accompaniedbypracticalexamples, adiscussion 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 biologiststhatwanttolearnhowtoanalyzeDNAsequencesinasimplebutmeaningful 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 throughtheweb.Mostchapterscouldbeusedforpracticaladvancedundergraduateor graduate-level courses in bioinformatics and molecular evolut

Spis treści

1. Similarity Searching Using BLAST Kit J. Menlove, Mark Clement, and Keith A. Crandall 2. Gene Orthology Assessment with OrthologID Mary Egan, Ernest K. Lee, Joanna C. Chiu, Gloria Coruzzi, and Rob DeSalle 3. Multiple Alignment of DNA Sequences with MAFFT Kazutaka Katoh, George Asimenos, and Hiroyuki Toh 4. SeqVis: A Tool for Detecting Compositional Heterogeneity among Aligned Nucleotide Sequences Lars Sommer Jermiin, Joshua Wing Kei Ho, Kwok-Wai Lau, and Vivek Jayaswal 5. Selection of Models of DNA Evolution with jModelTest David Posada 6. Estimating Maximum Likelihood Phylogenies with PhyML Stéphane Guindon, Frédéric Delsuc, Jean-François Dufayard, and Olivier Gascuel 7. Trees from Trees: Construction of Phylogenetic Supertrees Using Clann Christopher J. Creevey and James O. McInerney 8. Detecting Signatures of Selection from DNA Sequences Using Datamonkey Art F.Y. Poon, Simon D.W. Frost, and Sergei L. Kosakovsky Pond 9. Recombination Detection and Analysis Using RDP3 Darren P. Martin 10. CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition Jesse Zaneveld, Micah Hamady, Noboru Sueoka, and Rob Knight 11. Genetic Code Prediction for Metazoan Mitochondria with GenDecoder Federico Abascal, Rafael Zardoya, and David Posada 12. Computational Gene Annotation in New Genome Assemblies Using GeneID Enrique Blanco and Josep F. Abril 13. Promoter Analysis: Gene Regulatory Motif Identification with A-GLAM Leonardo Mariño-Ramírez, Kannan Tharakaraman, John L. Spouge, and David Landsman 14. Analysis of Genomic DNA with the UCSC Genome Browser Jonathan Pevsner 15. Mining forSNPs and SSRs using SNPServer, dbSNP and SSR Taxonomy Tree Jacqueline Batley and David Edwards 16. Analysis of Transposable Element Sequences Using CENSOR and RepeatMasker Ahsan Huda and I. King Jordan 17. DNA Sequence Polymorphism Analysis Using DnaSP Julio Rozas

Blurb

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.