Strings 2008 2 2: Difference between revisions
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== Pattern search == | == Pattern search == | ||
Text searching is an example of a simple problem with different algorithmic approaches. In practice most commonly one needs to check if a pattern is contained in a larger string, and if so at which location. | Text searching is an example of a simple problem with different algorithmic approaches. In practice most commonly one needs to check if a pattern (a short string) is contained in a larger string, and if so at which location. | ||
Despite the simplicity of the problem, it is frequently used in bioinformatics. | Despite the simplicity of the problem, it is frequently used in bioinformatics. | ||
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* Find [http://en.wikipedia.org/wiki/Restriction_enzyme restriction enzyme] cutting sites | * Find [http://en.wikipedia.org/wiki/Restriction_enzyme restriction enzyme] cutting sites | ||
* Search for [http://en.wikipedia.org/wiki/PCR PCR] primer matches | * Search for [http://en.wikipedia.org/wiki/PCR PCR] primer matches | ||
=== Formalisation of the problem === | |||
''Given a pattern p and a string s, find the first location where the pattern matches identically the string. If the pattern is not contained in the string report the outcome. | |||
'' | |||
The following sections describe basic search algorithms to locate a DNA fragment in a genome. But remember that the same concepts can be applied to any pattern/string pair. | The following sections describe basic search algorithms to locate a DNA fragment in a genome. But remember that the same concepts can be applied to any pattern/string pair. | ||
Revision as of 01:47, 10 January 2008
Pattern search
Text searching is an example of a simple problem with different algorithmic approaches. In practice most commonly one needs to check if a pattern (a short string) is contained in a larger string, and if so at which location.
Despite the simplicity of the problem, it is frequently used in bioinformatics. Examples:
- Find start (ATG) and stop (TAA, TGA and TGG) codons
- Find restriction enzyme cutting sites
- Search for PCR primer matches
Formalisation of the problem
Given a pattern p and a string s, find the first location where the pattern matches identically the string. If the pattern is not contained in the string report the outcome.
The following sections describe basic search algorithms to locate a DNA fragment in a genome. But remember that the same concepts can be applied to any pattern/string pair.
--ThomasHuber 12:28, 10 January 2008 (EST)
