Paper

LogoMotif: a comprehensive database of transcription factor binding site profiles in Actinobacteria

Augustijn, Hannah E, Joosten, Kristy, Medema, Marnix H, Karapliafis, Dimitris, Rigali, Sebastien, Van Wezel, Gilles P

2024

Overview

Actinobacteria undergo a complex multicellular life cycle and produce a wide range of specialized metabolites, including the majority of the antibiotics. These biological processes are controlled by intricate regulatory pathways, and to better understand how they are controlled we need to augment our insights into the transcription factor binding sites. Here, we present LogoMotif (https://logomotif.bioinformatics.nl), an open-source database for characterized and predicted transcription factor binding sites in Actinobacteria, along with their cognate position weight matrices and hidden Markov models. Genome-wide predictions of binding site locations in Streptomyces model organisms are supplied and visualized in interactive regulatory networks. In the web interface, users can freely access, download and investigate the underlying data. With this curated collection of actinobacterial regulatory interactions, LogoMotif serves as a basis for binding site predictions, thus providing users with clues on how to elicit the expression of genes of interest and guide genome mining efforts.Competing Interest StatementM.H.M. is a member of the Scientific Advisory Board of Hexagon Bio.

• Publisher: Cold Spring Harbor Laboratory Press,Cold Spring Harbor Laboratory
• Subject: Actinobacteria / Antibiotics / Binding sites / Bioinformatics / Genomes / Life cycles / Markov chains / Transcription factors