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E-raamat: Bioinformatics for DNA Sequence Analysis

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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,adiscussio n 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 evolution.
Preface vii
Contributors xi
Similarity Searching Using BLAST
1(22)
Kit J. Menlove
Mark Clement
Keith A. Crandall
Gene Orthology Assessment with Ortholog ID
23(16)
Mary Egan
Ernest K. Lee
Joanna C. Chiu
Gloria Coruzzi
Rob DeSalle
Multiple Alignment of DNA Sequences with MAFFT
39(26)
Kazutaka Kathoh
George Asimenos
Hiroyuki Toh
Seq Vis: A Tool for Detecting Compositional Heterogeneity Among Aligned Nucelotide Sequences
65(28)
Lars Sommer Jermiin
Joshua Wing Kei Ho
Kwok Wai Lau
Vivek Jayaswal
Selection of Models of DNA Evolution with jModel Test
93(20)
David Posada
Estimating Maximum Likelihood Phylogenies with PhyML
113(26)
Stephane Guindon
Frederic Delsuc
Jean-Francois Dufayard
Olivier Gascuel
Trees from Trees: Construction of Phylogenetic Supertrees Using Clann
139(24)
Christopher J. Creevey
James O. McInerney
Detecting Signatures of Selection from DNA Sequences Usign Datamonkey
163(22)
F.Y. Poon
Simon D.W. Frost
Sergei L. Kosakovsky Pond
Recombination Detection and Analysis Using RDP3
185(22)
Darren P. Martin
CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition
207(26)
Jesse Zaneveld
Micah Hamady
Noboru Sueoka
Rob Knight
Genetic Code Prediction for Metazoan Mitochondria with GenDecoder
233(10)
Federico Abascal
Rafael Zardoya
David Posada
Computational Gene Annotation in New Genome Assemblies Using GeneID
243(20)
Enrique Blanco
Josep F. Abril
Promoter Analysis: Gene Regulatory Motif Identification with A-GLAM
263(14)
Leonardo Marino-Ramirez
Kannan Tharakaraman
John L. Spouge
David Landsman
Analysis of Genomic DNA with teh UCSC Genome Browser
277(26)
Jonathan Pevsner
Mining for SNPs and SSRs Using SNPServer, dbSNP and SSR Taxonomy Tree
303(20)
Jacqueline Batley
David Edwards
Analysis of Transposable Element Sequences Using CENSOR and RepeatMasker
323(14)
Ahsan Huda
I. King Jordan
DNA Sequence Polymorphism Analysis Using DnaSP
337(14)
Julio Rozas
Index 351