[en] 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.
Disciplines :
Microbiology
Author, co-author :
Augustijn, Hannah E; Bioinformatics Group, Wageningen University, Wageningen, The Netherlands, Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
Karapliafis, Dimitris; Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
Joosten, Kristy M M; Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
Rigali, Sébastien ; Université de Liège - ULiège > Département des sciences de la vie
van Wezel, Gilles P; Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands. Electronic address: g.wezel@biology.leidenuniv.nl
Medema, Marnix H; Bioinformatics Group, Wageningen University, Wageningen, The Netherlands, Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands. Electronic address: marnix.medema@wur.nl
Language :
English
Title :
LogoMotif: A Comprehensive Database of Transcription Factor Binding Site Profiles in Actinobacteria.
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