TY - GEN
AB - We present a probabilistic interpretation of local sequence alignment methods where the alignment scoring system (ASS) plays the role of a stochastic process defining a probability distribution over all sequence pairs. An explicit algorithms is given to compute the probability of two sequences given and ASS. Based on this definition, a modified version of the Smith-Waterman local similarity search algorithm has been devised, which assesses sequence relationships by log likelihood ratios. When tested on classical examples such as globins or G-protein-coupled receptors, the new method proved to be up to an order of magnitude more sensitive than the native Smith-Waterman algorithm.
T1 - A sequence similarity search algorithm based on a probabilistic interpretation of an alignment scoring system
DA - 1996
AU - Bucher, P.
AU - Hofmann, K.
JF - Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology
SP - 44-51
VL - 4
EP - 44-51
ID - 176178
KW - Algorithms
KW - Models, Molecular
SN - 1553-0833
ER -