ArticleBMC bioinformatics2018
G4PromFinder: an algorithm for predicting transcription promoters in GC-rich bacterial genomes based on AT-rich elements and G-quadruplex motifs.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 41 citations in OpenAlex.
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- Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life.Genome research · 2025Article
- TSS-Captur: a user-friendly pipeline for characterizing unclassified RNA transcripts.NAR genomics and bioinformatics · 2024Article
- Recognition of cyanobacteria promoters via Siamese network-based contrastive learning under novel non-promoter generation.Briefings in bioinformatics · 2024Article
- Classification of Promoter Sequences from Human Genome.International journal of molecular sciences · 2023Article
- G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT)International journal of molecular sciences · 2023Article
- Database of Potential Promoter Sequences in theBiology · 2022Article
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- Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.Briefings in bioinformatics · 2022Article
- TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization ofFrontiers in genetics · 2022Article
- Promotech: a general tool for bacterial promoter recognition.Genome biology · 2021Article
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- Functional and Structural Characterization of Acquired 16S rRNA Methyltransferase NpmB1 Conferring Pan-Aminoglycoside Resistance.Antimicrobial agents and chemotherapy · 2021Article
- Deciphering the genetic code of DNA methylation.Briefings in bioinformatics · 2021Review
- How bioinformatics resources work with G4 RNAs.Briefings in bioinformatics · 2021Review
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- Use of Mathematical Methods for the Biosafety Assessment of Agricultural Crops.Applied biochemistry and microbiology · 2021Article
- A guide to computational methods for G-quadruplex prediction.Nucleic acids research · 2020Review
- Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences inMicroorganisms · 2019Article
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6 authors at 4 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundOver the last few decades, computational genomics has tremendously contributed to decipher biology from genome sequences and related data. Considerable effort has been devoted to the prediction of transcription promoter and terminator sites that represent the essential "punctuation marks" for DNA transcription. Computational prediction of promoters in prokaryotes is a problem whose solution is far from being determined in computational genomics. The majority of published bacterial promoter prediction tools are based on a consensus-sequences search and they were designed specifically for vegetative σ
resultsIn this study we investigated the possibility to identify putative promoters in prokaryotes based on evolutionarily conserved motifs, and focused our attention on GC-rich bacteria in which promoter prediction with conventional, consensus-based algorithms is often not-exhaustive. Here, we introduce G4PromFinder, a novel algorithm that predicts putative promoters based on AT-rich elements and G-quadruplex DNA motifs. We tested its performances by using available genomic and transcriptomic data of the model microorganisms Streptomyces coelicolor A3(2) and Pseudomonas aeruginosa PA14. We compared our results with those obtained by three currently available promoter predicting algorithms: the σ
conclusionsOur analysis shows that G4PromFinder is a powerful tool for promoter search in GC-rich bacteria, especially for bacteria coding for a lot of σ factors, such as the model microorganism S. coelicolor A3(2). Moreover consensus-based tools and, in general, tools that are based on specific features of bacterial σ factors seem to be less performing for promoter prediction in these types of bacterial genomes.
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