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Biological Sequences

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Encyclopedia of Database Systems

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Synonyms

DNA sequences; Protein sequence

Definition

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.

Cross-references

Index Structures for Biological Sequences

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Recommended Reading

  1. Brown A.L. Constructing genome scale suffix trees. In Proc. 2nd Asia-Pacific Bioinformatics Conference, 2004.

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  2. Hunt E., Atkinson M.P., and Irving R.W. A database index to large biological sequences. In Proc. 27th Int. Conf. on Very Large Data Bases, 2001, pp. 139–148.

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  3. Phoophakdee B. and Zaki M.J. TRELLIS +: an effective approach for indexing genome-scale sequences using suffix trees. In Proceedings of the Pacific Symposium on Biocomputing (online proceedings), 2008, pp. 90–101.

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  4. Tian Y., Tata S., Hankins R.A., and Patel J.M. Practical methods for constructing suffix trees. VLDB J., 14(3):281–299, 2005.

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Author information

Authors and Affiliations

  1. University of California-San Digeo, La Jolla, CA, USA

    Amarnath Gupta

Authors
  1. Amarnath Gupta
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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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Gupta, A. (2009). 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_1307

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