Optimal Alignments in Linear Space Using Automaton-derived Cost Functions (extended Abstract)

In a previous paper SM95], we showed how nite automata could be used to deene objective functions for assessing the quality of an alignment of two (or more) sequences. In this paper, we show some results of using such cost functions. We also show how to extend Hischberg's linear space algorithm Hir75] to this setting, thus generalizing a result of Myers and Miller MM88b].

[1]  Xiaojun Guan,et al.  Alignments of DNA and protein sequences containing frameshift errors , 1996, Comput. Appl. Biosci..

[2]  Brenda S. Baker,et al.  A theory of parameterized pattern matching: algorithms and applications , 1993, STOC.

[3]  James W. Fickett,et al.  Fast optimal alignment , 1984, Nucleic Acids Res..

[4]  Eugene W. Myers,et al.  Optimal alignments in linear space , 1988, Comput. Appl. Biosci..

[5]  D. Haussler,et al.  A hidden Markov model that finds genes in E. coli DNA. , 1994, Nucleic acids research.

[6]  J. Spouge.  Speeding up dynamic programming algorithms for finding optimal lattice paths , 1989 .

[7]  M. Held,et al.  Finite-State Processes and Dynamic Programming , 1967 .

[8]  Esko Ukkonen,et al.  Algorithms for Approximate String Matching , 1985, Inf. Control..

[9]  David Haussler,et al.  Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families , 1993, ISMB.

[10]  M. Bishop,et al.  Maximum likelihood alignment of DNA sequences. , 1986, Journal of molecular biology.

[11]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[12]  E. Myers,et al.  Sequence comparison with concave weighting functions. , 1988, Bulletin of mathematical biology.

[13]  A. Apostolio,et al.  A Fast Linear Space Algorithm for Computing Longest Common Subsequences , 1985 .

[14]  David B. Searls,et al.  Automata-Theoretic Models of Mutation and Alignment , 1995, ISMB.