ArticleBMC research notes2011
PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes.
Article in BMC research notes, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Construction and application of an insertional activation cloning vector.BMC biotechnology · 2026Article
- CDBProm: the Comprehensive Directory of Bacterial Promoters.NAR genomics and bioinformatics · 2024Article
- Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.Briefings in bioinformatics · 2022Article
- Identification, Functional Characterization, and Regulon Prediction of the Zinc Uptake Regulator (Frontiers in microbiology · 2018Article
- Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
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- Engineering the genome of Thermus thermophilus using a counterselectable marker.Journal of bacteriology · 2015Article
- Phenotypic Heterogeneity Affects Stenotrophomonas maltophilia K279a Colony Morphotypes and β-Lactamase Expression.Frontiers in microbiology · 2015Article
- Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs.Journal of computer-aided molecular design · 2014Article
- Transcriptome dynamics-based operon prediction in prokaryotes.BMC bioinformatics · 2014Article
- Functional characterization of WalRK: A two-component signal transduction system from Bacillus anthracis.FEBS open bio · 2014Article
- The genome organization of Thermotoga maritima reflects its lifestyle.PLoS genetics · 2013Article
- In silico method for modelling metabolism and gene product expression at genome scale.Nature communications · 2012Article
- Nucleic acids in disease and disorder: Understanding the language of life emerging from the 'ABC' of DNA.Journal of biosciences · 2012Article
- Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs.Journal of biosciences · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAs more and more genomes are being sequenced, an overview of their genomic features and annotation of their functional elements, which control the expression of each gene or transcription unit of the genome, is a fundamental challenge in genomics and bioinformatics.
findingsRelative stability of DNA sequence has been used to predict promoter regions in 913 microbial genomic sequences with GC-content ranging from 16.6% to 74.9%. Irrespective of the genome GC-content the relative stability based promoter prediction method has already been proven to be robust in terms of recall and precision. The predicted promoter regions for the 913 microbial genomes have been accumulated in a database called PromBase. Promoter search can be carried out in PromBase either by specifying the gene name or the genomic position. Each predicted promoter region has been assigned to a reliability class (low, medium, high, very high and highest) based on the difference between its average free energy and the downstream region. The recall and precision values for each class are shown graphically in PromBase. In addition, PromBase provides detailed information about base composition, CDS and CG/TA skews for each genome and various DNA sequence dependent structural properties (average free energy, curvature and bendability) in the vicinity of all annotated translation start sites (TLS).
conclusionPromBase is a database, which contains predicted promoter regions and detailed analysis of various genomic features for 913 microbial genomes. PromBase can serve as a valuable resource for comparative genomics study and help the experimentalist to rapidly access detailed information on various genomic features and putative promoter regions in any given genome. This database is freely accessible for academic and non- academic users via the worldwide web http://nucleix.mbu.iisc.ernet.in/prombase/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.