Alignment algorithm

WR Taylor. Multiple protein sequence alignment Algorithms and gap insertion. Methods Enzymol 266 343-367, 1996. 

The usual alignment algorithm fixes 0 and A as 0o and Aq, so that the prior is 1 when 0 = 00 and A = Aq and is 0 otherwise. Clearly, if experience justifies this choice or some other nonuniform choice, we can choose an informative prior that biases the calculation to certain values for the parameters or limits them to some likely range. The likelihood is well defined by the alignment model defined by using a similarity matrix and affine gap penalties, so that... 

A Zellner. An Introduction to Bayesian Inference in Econometrics. New York Wiley, 197L I Zhu, IS Em, CE Lawrence. Bayesian adaptive sequence alignment algorithms. Bioinformat-ics 14 25 -39, 1998. 

Pierce, K.M., Wood, L.F., Wright, B.M., Synovec, R.E. (2005). A comprehensive two-dimensional retention time alignment algorithm to enhance chemometric analysis of comprehensive two-dimensional separation data. Anal. Chem. 77, 7735-7743. 

We have analyzed the run-to-run reproducibility of the two-dimensional capillary electrophoresis system. The relative standard deviation in both MECC and CSE dimensions is better than 2% for the 50 most intense components in a set of five runs, and a simple gel alignment algorithm provides a twofold improvement in precision. 

By its size, this chapter fails to address the entire background of MQS and for more information, the reader is referred to several reviews that have been published on the topic. Also it could not address many related approaches, such as the density matrix similarity ideas of Ciosloswki and Fleischmann [79,80], the work of Leherte et al. [81-83] describing simplified alignment algorithms based on quantum similarity or the empirical procedure of Popelier et al. on using only a reduced number of points of the density function to express similarity [84-88]. It is worth noting that MQS is not restricted to the most commonly used electron density in position space. Many concepts and theoretical developments in the theory can be extended to momentum space where one deals with the three components of linear momentum... 

Bultinck, P., Carbo-Dorca, R. and Van Alsenoy, C. (2003) Quality of approximate electron densities and internal consistency of molecular alignment algorithms in molecular quantum similarity. 

Algorithmically, profile searching simply uses the dynamic programming alignment algorithm for aligning a sequence to a profile on each sequence... 

Waterman, M. S. (1984) Efficient sequence alignment algorithms,/. Theor. Biol. 108 333-337. 

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