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Encyclopedia of Database Systems pp 2261–2264Cite as

Query Languages and Evaluation Techniques for Biological Sequence Data

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Synonyms

Querying DNA sequences; Querying protein sequences

Definition

A common type of data that is used in life science applications is biological sequence data. Data such as DNA sequence and protein sequence data are growing at a very fast rate. For example, the data at GenBank[GB07] has been growing exponentially, doubling roughly every 18 months. These sequence datasets are often queried in complex ways and the methods required to query these sequences go far beyond the simple string matching methods that have been used in more traditional string applications. In order to enable users to easily pose sophisticated queries on these biological sequences, different languages have been designed to support a rich library of functions. In addition, some database systems have been extended to support a rich set of operators on the sequence data type. Compared to the stand-alone approach, the database method brings the power of algebraic query optimization and the use of indexes making it...

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Author information

Authors and Affiliations

  1. IBM Almaden Research Center, San Jose, CA, USA

    Sandeep Tata

  2. University of Wisconsin-Madison, Madison, WI, USA

    Jignesh M. Patel

Authors
  1. Sandeep Tata
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  2. Jignesh M. Patel
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Editor information

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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Tata, S., Patel, J.M. (2009). Query Languages and Evaluation Techniques for Biological Sequence Data. In: LIU, L., ÖZSU, M.T. (eds) Encyclopedia of Database Systems. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-39940-9_630

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