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Encyclopedia of Database Systems pp 287–288Cite as

Biological Sequences

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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.

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Recommended Reading

  1. Brown AL. Constructing genome scale suffix trees. In: Proceedings of the 2nd Asia-Pacific Bioinformatics Conference; 2004.

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  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.

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  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.

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  4. Tian Y, Tata S, Hankins RA, Patel JM. Practical methods for constructing suffix trees. VLDB J. 2005;14(3):281–99.

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA

    Amarnath Gupta

Authors
  1. Amarnath Gupta
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Corresponding author

Correspondence to Amarnath Gupta .

Editor information

Editors and Affiliations

  1. Georgia Institute of Technology College of Computing, Atlanta, GA, USA

    Ling Liu

  2. University of Waterloo School of Computer Science, Waterloo, ON, Canada

    M. Tamer Özsu

Section Editor information

  1. San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA

    Amarnath Gupta

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Gupta, A. (2018). Biological Sequences. In: Liu, L., Özsu, M.T. (eds) Encyclopedia of Database Systems. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8265-9_1307

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