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Encyclopedia of Database Systems pp 1428–1432Cite as

Index Structures for Biological Sequences

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Definition

Biological sequence databases are mainly composed of DNA, RNA, and protein sequences. DNA and RNA sequences are polymers of nucleotides, whereas proteins are polymers of amino acids. A database of biological sequences contains a set of biological sequences of the same type. The length of each sequence varies from less than a hundred to several hundred million bases. An index structure on a database of biological sequences helps in identifying sequences in that database that are similar to a given query sequence quickly. The definition of similarity depends on two orthogonal parameters; similarity function and the length of the similarity of interest.

The simplest similarity function is the edit distance, which measures the number of substitutions, insertions, and deletions needed to transform one sequence to the other. More complex functions involve variable gap penalties and substitution scores based on how frequent substitutions are observed in nature. The length of the...

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Authors and Affiliations

    Authors
    1. Tamer Kahveci
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    Editors and Affiliations

    1. College of Computing, Georgia Institute of Technology, 266 Ferst Drive, 30332-0765, Atlanta, GA, USA

      LING LIU (Professor) (Professor)

    2. Database Research Group David R. Cheriton School of Computer Science, University of Waterloo, 200 University Avenue West, N2L 3G1, Waterloo, ON, Canada

      M. TAMER ÖZSU (Professor and Director, University Research Chair) (Professor and Director, University Research Chair)

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    © 2009 Springer Science+Business Media, LLC

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    Kahveci, T. (2009). Index Structures for Biological Sequences. In: LIU, L., ÖZSU, M.T. (eds) Encyclopedia of Database Systems. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-39940-9_1434

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