ArticleBioinformatics (Oxford, England)2010
Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Interfacial water confers transcription factors with dinucleotide specificity.Nature structural & molecular biology · 2025Article
- The PhoPQ Two-Component System Is the Major Regulator of Cell Surface Properties, Stress Responses and Plant-Derived Substrate Utilisation During Development ofFrontiers in microbiology · 2020Article
- Global transcriptional regulator TrmB family members in prokaryotes.Journal of microbiology (Seoul, Korea) · 2016Review
- Assessment of transfer methods for comparative genomics of regulatory networks in bacteria.BMC bioinformatics · 2016Article
- σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough.BMC genomics · 2015Article
- An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria.Journal of bacteriology · 2015Article
- Substrate-dependent activation of the Vibrio cholerae vexAB RND efflux system requires vexR.PloS one · 2015Article
- Article
- IntergenicDB: a database for intergenic sequences.Bioinformation · 2014Article
- Comparative genomics and evolution of regulons of the LacI-family transcription factors.Frontiers in microbiology · 2014Article
- Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes.Journal of bacteriology · 2013Article
- Rationally designed families of orthogonal RNA regulators of translation.Nature chemical biology · 2012Article
- Genome context as a predictive tool for identifying regulatory targets of the TetR family transcriptional regulators.PloS one · 2012Article
- Quantifying the sequence-function relation in gene silencing by bacterial small RNAs.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Article
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2 authors.
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Abstract
motivationComputational techniques for microbial genomic sequence analysis are becoming increasingly important. With next-generation sequencing technology and the human microbiome project underway, current sequencing capacity is significantly greater than the speed at which organisms of interest can be studied experimentally. Most related computational work has been focused on sequence assembly, gene annotation and metabolic network reconstruction. We have developed a method that will primarily use available sequence data in order to determine prokaryotic transcription factor (TF) binding specificities.
resultsSpecificity determining residues (critical residues) were identified from crystal structures of DNA-protein complexes and TFs with the same critical residues were grouped into specificity classes. The putative binding regions for each class were defined as the set of promoters for each TF itself (autoregulatory) and the immediately upstream and downstream operons. MEME was used to find putative motifs within each separate class. Tests on the LacI and TetR TF families, using RegulonDB annotated sites, showed the sensitivity of prediction 86% and 80%, respectively. AVAILABILITY: http://ural.wustl.edu/∼gsahota/HTHmotif/
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