Chapter 8. Sequence Alignment and Database Searching

  1. Andreas D. Baxevanis2 and
  2. B. F. Francis Ouellette3
  1. Gregory D. Schuler

Published Online: 11 JAN 2002

DOI: 10.1002/0471223921.ch8

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Volume 43, Second Edition

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Volume 43, Second Edition

How to Cite

Schuler, G. D. (2001) Sequence Alignment and Database Searching, in Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Volume 43, Second Edition (eds A. D. Baxevanis and B. F. F. Ouellette), John Wiley & Sons, Inc., New York, USA. doi: 10.1002/0471223921.ch8

Editor Information

  1. 2

    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland

  2. 3

    Centre for Molecular Medicine and Therapeutics, Children's and Women's Health Centre of British Columbia, University of British Columbia Vancouver, British Columbia, Canada

Author Information

  1. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland

Publication History

  1. Published Online: 11 JAN 2002
  2. Published Print: 20 APR 2001

ISBN Information

Print ISBN: 9780471383901

Online ISBN: 9780471223924

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Keywords:

  • sequence alignment;
  • evolutionary basis;
  • proteins;
  • optimal alignment methods;
  • substitution scores;
  • gap penalties;
  • similarity searching;
  • FASTA;
  • BLAST;
  • database searching artifacts;
  • scoring matrices;
  • spliced alignments

Summary

This chapter is an overview of methods available for detecting similarities between two biological sequences. The emphasis of this chapter is the use of the BLAST family of programs in doing meaningful homology searches. A problem set appears at the end of the chapter.