Bacterial promoter consensus sequences1/16/2024 Plus a huge database of transcriptional units. BMC Genomics 13:299).ĭOOR3 - Database of pr Okaryotic Ope Rons - offers high-performance web service for online operon prediction on user-provided genomic sequences and, an intuitive genome browser to support visualization of user-selected data. PePPER (University of Groningen, The Netherlands) is a webserver for prediction of prokaryote promoter elements and regulons ( Reference: de Yong, A. Virtual Footprint - offers two types of analyses (a) Regulon Analysis - analysis of a whole prokaryotic genome with one regulator pattern and (b) Promoter analysis - Analysis of a promoter region with several regulator patterns ( Reference: R. 12(2): e0171410).ĭeep Learning Recognition using Convolutional Neural Networks (CNNPromoter & CNNProm) - Classification of Prokaryotic and Eukaryotic Promoters and non-promoter sequences ( Reference: Umarov R.K & Solovyev V.V. ( Reference: Umarov RK, & Solovyev VV (2017) PLoS One. 61-78)ĬNNPromoter_b - Prediction of Bacterial Promoters by CNN models in genomic sequences. In Metagenomics and its Applications in Agriculture, Biomedicine and Environmental Studies (Ed. Solovyev & A Salamov (2011) Automatic Annotation of Microbial Genomes and Metagenomic Sequences. IPro54-PseKNC - is a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition. I would recommend using <100 nt upstream from the start codon. IPro70-PseZNC - is a tool for identifying σ70 promoters with novel pseudo nucleotide composition ( Reference: Lai H-Y et al. 35(24): 5301-5302).īacPP: Bacterial Promoter Prediction - A tool for accurate sigma-factor specific assignment in enterobacteria. It is part of Galaxy.( Reference: Sampaio M et al. This is the first online tool for predicting promoters that uses phage promoter data and the first to identify both host and phage promoters with different motifs. PhagePromoter - is a tool for locating promoters in phage genomes, using machine learning methods. PromoterHunter - is part of phiSITE database which is a collection of phage gene regulatory elements, genes, genomes and other related information, plus tools. SAPPHIRE Sequence Analyser for the Prediction of Prokaryote Homology Inferred Regulatory Elements - is a neural network based classifier for σ70 promoter prediction in Pseudomonas ( Reference: Coppens L & Lavigne R (2020) BMC Bioinformatics 21(1): 415).ħ0ProPred - is a predictor for discovering sigma70 promoters based on combining multiple features including position-specific trinucletide propensity (PSTNP) feature extraction in combination with the electron-ion interaction pseudopotentials (EIIPs) of nucleotides. Online Analysis Tools - Promoters PROMOTERS & TERMINATORS
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