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Detecting protein homology using NCBI tools

Part 4. Bioinformatics

4.8. Modern Programming Paradigms in Biology

Introductory Review

  1. Wayne T. Matten,
  2. Scott D. McGinnis

Published Online: 15 JAN 2005

DOI: 10.1002/047001153X.g409113

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Matten, W. T. and McGinnis, S. D. 2005. Detecting protein homology using NCBI tools. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.8:93.

Author Information

  1. National Center for Biotechnology Information, Bethesda, MD, USA

Publication History

  1. Published Online: 15 JAN 2005

Abstract

The National Center for Biotechnology Information (NCBI) processes more than 100 000 sequence similarity searches a day using the computer program, BLAST® – Basic Local Alignment Search Tool. A common use of BLAST is to locate sequences in the NCBI databases that are related to the query sequence. Various “flavors” of BLAST can also detect known conserved domains in the query sequence, find related sequences that contain a supplied pattern, and perform sensitive searches using automated construction of position-specific scoring matrices. The results of precomputed BLAST searches are available for nearly all protein sequences housed at the NCBI. Similarly, solved protein structures are compared to identify structurally related proteins using the Vector Alignment Search Tool (VAST).

Keywords:

  • BLAST;
  • sequence similarity;
  • homology;
  • NCBI;
  • VAST