Bioinformatics for DNA Sequence Analysis.pdf - Index of

Chapter 1Similarity Searching Using BLASTKit J. Menlove, Mark Clement, and Keith A. CrandallAbstractSimilarity searches are an essential component of most bioinformatic applications. They form the bases ofstructural motif identification, gene identification, and insights into functional associations. With the rapidincrease in the available genetic data through a wide variety of databases, similarity searches are an essentialtool for accessing these data in an informative and productive way. In this chapter, we provide an overviewof similarity searching approaches, related databases, and parameter options to achieve the best results for avariety of applications. We then provide a worked example and some notes for consideration.Key words: BLAST, sequence alignment, similarity search.1. Introduction1.1. An Introduction toNucleotide DatabasesPerhaps the central goal of genetics is to articulate the associationsof phenotypes of interest with their underlying genetic componentsand then to understand the relationship between geneticvariation and variation in the phenotype. This goal has beenbuoyed by the tremendous increase in our ability to obtain moleculargenetic data, across both populations and species. As methodsof gathering information about various aspects of biologicalmacromolecules arose, biological information became abundantand the need to consolidate and make this information accessiblebecame increasingly apparent. In the early 1960s, Margaret Dayhoffand colleagues at the National Biomedical Research Foundation(NBRF) began collecting information on protein sequencesand structure into a volume entitled Atlas of Protein Sequence andStructure (1). Since that beginning, databases have been an importantand essential part of biological and biochemical research.David Posada (ed.), Bioinformatics for DNA Sequence Analysis, Methods in Molecular Biology 537ª Humana Press, a part of Springer ScienceþBusiness Media, LLC 2009DOI 10.1007/978-1-59745-251-9_11