dipwmsearch: a python package for searching di-PWM motifs

Abstract

MotivationSeeking probabilistic motifs in a sequence is a common task to annotate putative transcription factor binding sites (TFBS). Useful motif representations include Position Weight Matrices (PWMs), dinucleotidic PWMs (di-PWMs), and Hidden Markov Models (HMMs). Dinucleotidic PWMs combine the simplicity of PWMs - a matrix form and a cumulative scoring function -, but also incoporate 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 di-PWMs in sequences. ResultsWe propose a Python package, dipwmsearch, which provides an original and efficient algorithm for this task (it first enumerates matching words for the di-PWM, and then search them at once in the sequence even if it contains IUPAC codes). The user benefits from an easy installation via Pypi or conda, a documented Python interface, and reusable example scripts that smooth the use of di-PWMs. Availability and Implementationdipwmsearch is available at https://pypi.org/project/dipwmsearch/ and https://gite.lirmm.fr/rivals/dipwmsearch/ under Cecill license.