dipwmsearch: a Python package for searching di-PWM motifs

Abstract

Motivation: Seeking probabilistic motifs in a sequence is a common task to annotate putative transcription factor binding sites or other RNA/DNA binding sites. Useful motif representations include position weight matrices (PWMs), dinucleotide PWMs (di-PWMs), and hidden Markov models (HMMs). Dinucleotide PWMs not only combine the simplicity of PWMs—a matrix form and a cumulative scoring function—but also incorporate dependency between adjacent positions in the motif (unlike PWMs which disregard any dependency). For instance to represent binding sites, the HOCOMOCO database provides di-PWM motifs derived from experimental data. Currently, two programs, SPRy-SARUS and MOODS, can search for occurrences of di-PWMs in sequences. Results: We propose a Python package called dipwmsearch, which provides an original and efficient algorithm for this task (it first enumerates matching words for the di-PWM, and then searches these all at once in the sequence, even if the latter contains IUPAC codes). The user benefits from an easy installation via Pypi or conda, a comprehensive documentation, and executable scripts that facilitate the use of di-PWMs.