User:Jarle Pahr/Algorithms: Difference between revisions
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Needleman–Wunsch algorithm: | Needleman–Wunsch algorithm: | ||
Dynamic programming algorithm to perform global sequence alignment. Also referred to as the "optimal matching algorithm". | |||
http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm | http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm | ||
In general parlance, a Needleman-Wunsch type algorithm refers to a global alignment algorithm that takes quadratic time for a linear or affine gap penalty. | |||
Revision as of 11:08, 31 March 2013
Notes on algorithms with use in bioinformatics and computational biology:
See also:
http://bix.ucsd.edu/bioalgorithms/
http://en.wikipedia.org/wiki/Category:Bioinformatics_algorithms
https://www.coursera.org/course/bioinformatics
Simplex algorithm:
Needleman–Wunsch algorithm:
Dynamic programming algorithm to perform global sequence alignment. Also referred to as the "optimal matching algorithm".
http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
In general parlance, a Needleman-Wunsch type algorithm refers to a global alignment algorithm that takes quadratic time for a linear or affine gap penalty.
Smith Waterman algorithm:
http://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm
See also http://seqanswers.com/forums/showthread.php?t=25305 for a discussion on implementing SW.
Burrows-Wheeler transform:
Misc:
http://www.cse.sc.edu/~maxal/csce590b/Lect01-02.pdf
Books:
http://www.amazon.com/Bioinformatics-Algorithms-Techniques-Applications-Wiley/dp/0470097736