Summary: String Matching
String matching: definition of the problem (text,pattern)
depends on what we have: text or patterns· Exact matching:
· Approximate matching:
· 1 pattern ---> The algorithm depends on |p| and | |
· k patterns ---> The algorithm depends on k, |p| and | |
· The text ----> Data structure for the text (suffix tree, ...)
· The patterns ---> Data structures for the patterns
· Dynamic programming
· Sequence alignment (pairwise and multiple)
· Extensions
· Regular Expressions
· Probabilistic search:
· Sequence assembly: hash algorithm
Hidden Markov Models
Approximate string matching
For instance, given the sequence
CTACTACTACGTGACTAATACTGATCGTAGCTAC...
search for the pattern ACTGA allowing one error...
... but what is the meaning of "one error"?

Source: Arias, Marta - Departament of Llenguatges i Sistemes Informátics, Universitat Politècnica de Catalunya

Collections: Computer Technologies and Information Sciences