A context dependent method for comparing sequences
Document Type
Conference Proceeding
Publication Date
1-1-1994
Department
Department of Computer Science
Abstract
A scoring scheme is presented to measure the similarity score between two biological sequences, where matches are weighted dependent on their context. The scheme generalizes a widely used scoring scheme. A dynamic programming algorithm is developed to compute a largest-scoring alignment of two sequences of lengths m and n in O(ran) time and O(m+n) space. Also developed is an algorithm for computing a largest-scoring local alignment between two sequences in quadratic time and linear space. Both algorithms are implemented as portable C programs. An experiment is conducted to compare protein alingments produced by the new global alignment program with ones by an existing program.
Publication Title
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Recommended Citation
Huang, X.
(1994).
A context dependent method for comparing sequences.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
807 LNCS, 54-63.
http://doi.org/10.1007/3-540-58094-8_5
Retrieved from: https://digitalcommons.mtu.edu/michigantech-p/4011