The computational linguistics of biological sequences
Artificial intelligence and molecular biology
Pattern Discovery in Biosequences
ICGI '98 Proceedings of the 4th International Colloquium on Grammatical Inference
A minimum description length approach to grammar inference
Connectionist, Statistical, and Symbolic Approaches to Learning for Natural Language Processing
Homology assessment and molecular sequence alignment
Journal of Biomedical Informatics - Special issue: Phylogenetic inferencing: Beyond biology
The fragment assembly string graph
Bioinformatics
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This paper presents a new information theoretic framework for aligning sequences in bioinformatics. A transmitter compresses a set of sequences by constructing a regular expression that describes the regions of similarity in the sequences. To retrieve the original set of sequences, a receiver generates all strings that match the expression. An alignment algorithm uses minimum description length to encode and explore alternative expressions; the expression with the shortest encoding provides the best overall alignment. When two substrings contain letters that are similar according to a substitution matrix, a code length function based on conditional probabilities defined by the matrix will encode the substrings with fewer bits. In one experiment, alignments produced with this new method were found to be comparable to alignments from CLUSTALW. A second experiment measured the accuracy of the new method on pairwise alignments of sequences from the BAliBASE alignment benchmark.