Encyclopedia of Database Systems

2018 Edition
| Editors: Ling Liu, M. Tamer Özsu

Index Structures for Biological Sequences

  • Tamer KahveciEmail author
Reference work entry
DOI: https://doi.org/10.1007/978-1-4614-8265-9_1434


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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.University of FloridaGainesvilleUSA

Section editors and affiliations

  • Louiqa Raschid
    • 1
  1. 1.Robert H. Smith School of BusinessUniversity of MarylandCollege ParkUSA