Article ID Journal Published Year Pages File Type
975673 Physica A: Statistical Mechanics and its Applications 2007 9 Pages PDF
Abstract
We construct a metric measure among weight matrices that are commonly used in non-interacting statistical physics systems, computational biology problems, as well as in general applications such as hidden Markov models. The metric distance between two weight matrices is obtained via aligning the matrices and thus can be evaluated by dynamic programming. Capable of allowing reverse complements in distance evaluation, this metric accommodates both gapless and gapped alignments between two weight matrices. The distance statistics among random motifs is also studied. We find that the average square distance and its standard error grow with different powers of motif length, and the normalized square distance follows a Gaussian distribution for large motif lengths.
Related Topics
Physical Sciences and Engineering Mathematics Mathematical Physics
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