Strings 2008 2 2
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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.
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
The following section describes 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.
