SeqTU (RNA-seq Based Transcription Unit Finder for Prokaryotes) - is a recently developed machine-learning method to accurately identify TUs from RNA-seq data, based on two features of the assembled RNA reads: the continuity and stability of RNA-seq coverage across a genomic region. patvic.txt output file to find where they are (Jan Mrázek, personal communication). You can restrict the search to intergenic regions (but this will eliminate also matches that partially overlap with genes or use the. If you only want one strand screened omit the at the start. the allows for 4 mismatches - I recommend a maximum of two. 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.
Library hunter citation tools plus#
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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