Large deviation properties for patterns

Abstract

Deciding whether a given pattern is overrepresented or under-represented according to a given background model is a key question in computational biology. Such a decision is usually made by computing some p-values reflecting the "exceptionality" of a pattern in a given sequence or set of sequences. In the simplest cases (short and simple patterns, simple background model, small number of sequences), an exact p-value can be computed with a tractable complexity. The realistic cases are in general too complicated to get such an exact p-value. Approximations are thus proposed (Gaussian, Poisson, Large deviation approximations). These approximations are applicable under some conditions: Gaussian approximations are valid in the central domain while Poisson and Large deviations approximations are valid for rare events. In the present paper, we prove a large deviation approximation to the double strands counting problem that refers to a counting of a given pattern in a set of sequences that arise from both strands of the genome. Here dependencies between a sequence and its complement plays a fundamental role. General combinatorial properties of the pattern allow to deal with such a dependency. A large deviation result is also provided for a set of small sequences.