1990 BasicLocalAlignmentSearchTool

• (Altschul et al., 1990) ⇒ Stephen F. Altschul, Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman. (1990). “Basic Local Alignment Search Tool.” In: Journal Molecular Biology, 215(3).

Subject Headings: BLAST Algorithm, BLAST System, Sequence Alignment Algorithm, Highly-Cited Paper.

Notes

• It relates to: (Smith & Waterman, 1981).
• It defines a Maximal Segment Pair Score.

Cited By

• http://scholar.google.com/scholar?cites=11606922962546801235

2009

• (Wikipedia, 2009) ⇒ http://en.wikipedia.org/wiki/BLAST#BLAST
  • The main idea of BLAST is that there are often high-scoring segment pairs (HSP) contained in a statistically significant alignment. BLAST searches for high scoring sequence alignments between the query sequence and sequences in the database using a heuristic approach that approximates the Smith-Waterman algorithm. The exhaustive Smith-Waterman approach is too slow for searching large genomic databases such as GenBank. Therefore, the BLAST algorithm uses a heuristic approach that is less accurate than the Smith-Waterman but over 50 times faster. The speed and relatively good accuracy of BLAST are among the key technical innovation of the BLAST programs.

Quotes

Abstract

A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.,

	Author	volume	Date Value	title	type	journal	titleUrl	doi	note	year
1990 BasicLocalAlignmentSearchTool	David J. Lipman Stephen F. Altschul Warren Gish Webb Miller Eugene W. Myers			Basic Local Alignment Search Tool		Journal Molecular Biology	http://www-math.mit.edu/~lippert/18.417/papers/altschuletal1990.pdf			1990