Book Volume 537 2009

Bioinformatics for DNA Sequence Analysis

Editors:

ISBN: 978-1-58829-910-9 (Print) 978-1-59745-251-9 (Online)

Table of contents (17 protocols)

  1. Front Matter

    Pages i-xiii

  2. No Access

    Protocol

    Pages 1-22

    Similarity Searching Using BLAST

  3. No Access

    Protocol

    Pages 23-38

    Gene Orthology Assessment with OrthologID

  4. No Access

    Protocol

    Pages 39-64

    Multiple Alignment of DNA Sequences with MAFFT

  5. No Access

    Protocol

    Pages 65-91

    SeqVis: A Tool for Detecting Compositional Heterogeneity Among Aligned Nucleotide Sequences

  6. No Access

    Protocol

    Pages 93-112

    Selection of Models of DNA Evolution with jModelTest

  7. No Access

    Protocol

    Pages 113-137

    Estimating Maximum Likelihood Phylogenies with PhyML

  8. No Access

    Protocol

    Pages 139-161

    Trees from Trees: Construction of Phylogenetic Supertrees Using Clann

  9. No Access

    Protocol

    Pages 163-183

    Detecting Signatures of Selection from DNA Sequences Using Datamonkey

  10. No Access

    Protocol

    Pages 185-205

    Recombination Detection and Analysis Using RDP3

  11. No Access

    Protocol

    Pages 207-232

    CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition

  12. No Access

    Protocol

    Pages 233-242

    Genetic Code Prediction for Metazoan Mitochondria with GenDecoder

  13. No Access

    Protocol

    Pages 243-261

    Computational Gene Annotation in New Genome Assemblies Using GeneID

  14. No Access

    Protocol

    Pages 263-276

    Promoter Analysis: Gene Regulatory Motif Identification with A-GLAM

  15. No Access

    Protocol

    Pages 277-301

    Analysis of Genomic DNA with the UCSC Genome Browser

  16. No Access

    Protocol

    Pages 303-321

    Mining for SNPs and SSRs Using SNPServer, dbSNP and SSR Taxonomy Tree

  17. No Access

    Protocol

    Pages 323-336

    Analysis of Transposable Element Sequences Using CENSOR and RepeatMasker

  18. No Access

    Protocol

    Pages 337-350

    DNA Sequence Polymorphism Analysis Using DnaSP

  19. Back Matter

    Pages 351-354