Dataset Information

SAPPHIRE: a neural network based classifier for ?70 promoter prediction in Pseudomonas.

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 ?70 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 ?70 promoters found experimentally in P. aeruginosa and P. putida. SAPPHIRE currently outperforms established predictive software when classifying Pseudomonas ?70 promoters and was built to allow further expansion in the future. CONCLUSIONS:SAPPHIRE is the first predictive tool for bacterial ?70 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.

SUBMITTER: Coppens L

PROVIDER: S-EPMC7510298 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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SAPPHIRE: a neural network based classifier for σ70 promoter prediction in Pseudomonas.

Coppens Lucas L Lavigne Rob R

BMC bioinformatics 20200922 1

<h4>Background</h4>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 bac ...[more]

PMID: 32962628

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Dataset Information

SAPPHIRE: a neural network based classifier for ?70 promoter prediction in Pseudomonas.

Publications

SAPPHIRE: a neural network based classifier for σ70 promoter prediction in Pseudomonas.

Similar Datasets

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