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 Phylogenetic Supertrees Using Clann -- Detecting Signatures of Selection from DNA Sequences Using 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 Using SNPServer, dbSNP and SSR Taxonomy Tree -- Analysis of Transposable Element Sequences Using CENSOR and RepeatMasker -- DNA Sequence Polymorphism Analysis Using DnaSP.

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.