Exact calculation of distributions on integers, with application to sequence alignment.

ABSTRACT: Computational biology is replete with high-dimensional discrete prediction and inference problems. Dynamic programming recursions can be applied to several of the most important of these, including sequence alignment, RNA secondary-structure prediction, phylogenetic inference, and motif finding. In these problems, attention is frequently focused on some scalar quantity of interest, a score, such as an alignment score or the free energy of an RNA secondary structure. In many cases, score is naturally defined on integers, such as a count of the number of pairing differences between two sequence alignments, or else an integer score has been adopted for computational reasons, such as in the test of significance of motif scores. The probability distribution of the score under an appropriate pro

SUBMITTER: Newberg LA 

PROVIDER: S-EPMC2858568 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature