Encyclopedia of Database Systems

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

Biological Sequences

  • Amarnath GuptaEmail author
Reference work entry
DOI: https://doi.org/10.1007/978-1-4614-8265-9_1307


DNA sequences; Protein sequence


A biological sequence is a sequence with a small fixed alphabet, and represents a naturally occurring or experimental generated fragment of genetic or protein material or any intermediate product (like the messenger RNA).

Example: A DNA fragment has the 4 character alphabet ‘A’, ‘C’, ‘T’, ‘G’. Chromosomes are long strings over this alphabet.

Key Points

Biological sequences can be long. A full chromosome may have millions of characters. Therefore development of proper storing and indexing strategies is very important for fast retrieval. Suffix tree based indexes have been used successfully for long biological sequences. Further, approximate string matching techniques with potential deletions and insertions are important for biological sequences. BLAST is a well known algorithm used for approximate matching and ranking of biological sequences.


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Recommended Reading

  1. 1.
    Brown AL. Constructing genome scale suffix trees. In: Proceedings of the 2nd Asia-Pacific Bioinformatics Conference; 2004.Google Scholar
  2. 2.
    Hunt E, Atkinson MP, Irving RW. A database index to large biological sequences. In: Proceedings of the 27th International Conference on Very Large Data Bases; 2001. p. 139–48.Google Scholar
  3. 3.
    Phoophakdee B, Zaki MJ. TRELLIS +: an effective approach for indexing genome-scale sequences using suffix trees. In: Proceedings of the Pacific Symposium on Biocomputing (online proceedings); 2008. p. 90–101.Google Scholar
  4. 4.
    Tian Y, Tata S, Hankins RA, Patel JM. Practical methods for constructing suffix trees. VLDB J. 2005;14(3):281–99.CrossRefGoogle Scholar

Copyright information

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

Authors and Affiliations

  1. 1.San Diego Supercomputer CenterUniversity of California San DiegoLa JollaUSA

Section editors and affiliations

  • Amarnath Gupta
    • 1
  1. 1.San Diego Supercomputer CenterUniversity of California San DiegoLa JollaUSA