Abstract
Abstract
Background
In silico promoter prediction represents an important challenge in bioinformatics as it provides a first-line approach to identifying regulatory elements to support wet-lab experiments. Historically, available promoter prediction software have focused on sigma factor-associated promoters in the model organism E. coli. As a consequence, traditional promoter predictors yield suboptimal predictions when applied to other prokaryotic genera, such as Pseudomonas, a Gram-negative bacterium of crucial medical and biotechnological importance.
Results
We developed SAPPHIRE, a promoter predictor for σ70 promoters in Pseudomonas. This promoter prediction relies on an artificial neural network that evaluates sequences on their similarity to the − 35 and − 10 boxes of σ70 promoters found experimentally in P. aeruginosa and P. putida. SAPPHIRE currently outperforms established predictive software when classifying Pseudomonas σ70 promoters and was built to allow further expansion in the future.
Conclusions
SAPPHIRE is the first predictive tool for bacterial σ70 promoters in Pseudomonas. SAPPHIRE is free, publicly available and can be accessed online at www.biosapphire.com. Alternatively, users can download the tool as a Python 3 script for local application from this site.
Funder
H2020 European Research Council
Publisher
Springer Science and Business Media LLC
Subject
Applied Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Structural Biology
Reference16 articles.
1. Bailey T, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology; 1994. p. 28–36.
2. Blasdel BG, Ceyssens P-J, Chevallereau A, Debarbieux L, Lavigne R. Comparative transcriptomics reveals a conserved bacterial adaptive phage response (BAPR) to viral predation. Cold Spring Harbor Lab. 2018. https://doi.org/10.1101/248849.
3. Domínguez-Cuevas P, Marqués S. Compiling sigma-70-dependent promoters. In: Ramos J-L, editor. Virulence and gene regulation. New York: Springer; 2004. p. 319–43.
4. Lavigne R, Lecoutere E, Wagemans J, Cenens W, Aertsen A, Schoofs L, et al. A Multifaceted Study of Pseudomonas aeruginosa Shutdown by Virulent Podovirus LUZ19. Vidaver AK, editor. mBio. 2013;4(2). https://doi.org/10.1128/mBio.00061-13.
5. Loeschcke A, Thies S. Pseudomonas putida-a versatile host for the production of natural products. Appl Microbiol Biotechnol. 2015;99:6197–214.
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