DNA duplex stability as discriminative characteristic for Escherichia coli σ54- and σ28- dependent promoter sequences

Ramprakash, 2008, Energetic contributions to the initiation in E. coli, Biophys Chem, 138, 91, 10.1016/j.bpc.2008.09.007 Hook-Barnard, 2006, Escherichia coli RNA polymerase enzyme of σ70- dependent promoter requiring a −35 DNA element and an extended −10 TGn motif, J Bacteriol, 188, 8352, 10.1128/JB.00853-06 Huffmann, 2002, Prokaryotic transcription regulators: more than just the helix-turn-helix motif, Curr Opin Struct Biol, 12, 98, 10.1016/S0959-440X(02)00295-6 Borukhov, 2008, RNA polymerase: the vehicle of transcription, Trends Microbiol, 16, 126, 10.1016/j.tim.2007.12.006 de Avila e Silva, 2012, Bacterial promoter features description and their application on E. coli in silico prediction and recognition approaches, 241 Potvin, 2008, Sigma factors in Pseudomonas aeruginosa, Feder Eur Microbiol Soc, 32, 38 Janga, 2007, Structure and evolution of gene regulatory networks in microbial genomes, Res Microbiol, 158, 787, 10.1016/j.resmic.2007.09.001 Jacques, 2006, Detection of prokaryotic promoters from the genomic ditribution of hexanucleotides pairs, BMC Bioinform, 7, 423, 10.1186/1471-2105-7-423 Towsey, 2008, The cross-species prediction of bacterial promoters using a support vector machine, Comput Biol Chem, 32, 359, 10.1016/j.compbiolchem.2008.07.009 Polate, 2007, A novel approach to estimation of E. coli promoter gene sequences: combining feature selection and least square support vector machine (FS_LSSVN), Appl Math Comput, 190, 1574, 10.1016/j.amc.2007.02.033 Li, 2006, The recognition and prediction of σ70 promoters in Escherichia coli K-12, J Theor Biol, 242, 135, 10.1016/j.jtbi.2006.02.007 Gordon, 2003, Sequence alignment for recognition of promoter regions, Bioinformatics, 19, 1964, 10.1093/bioinformatics/btg265 Burden, 2005, Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences, Bioinformatics, 21, 601, 10.1093/bioinformatics/bti047 de Avila e Silva, 2011, BacPP: bacterial promoter prediction—a tool for accurate sigma-factor specific assignment in enterobacteria, J Theor Biol, 287, 92, 10.1016/j.jtbi.2011.07.017 Kalate, 2003, Artificial neural networks for prediction of mycobaterial promoter sequences, Comput Biol Chem, 27, 555, 10.1016/j.compbiolchem.2003.09.004 Rani, 2007, Analysis of E. coli promoter recognition problem in dinucleotide feature space, Bioinformatics, 23, 582, 10.1093/bioinformatics/btl670 Askary, 2009, N4: a precise and highly sensitive promoter predictor using neural network fed by nearest neighbors, Genes Genet Syst, 84, 425, 10.1266/ggs.84.425 Odajima, 2008, Greedy rule generation from discrete data and its use in neural network rule extraction, Neural Networks, 21, 1020, 10.1016/j.neunet.2008.01.003 Andrews, 1995, A survey and critique of techniques for extracting rules from trained artificial neural networks, Knowledge-Based Syst, 8, 373, 10.1016/0950-7051(96)81920-4 Kanhere, 2005, Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes, Nucleic Acids Res, 33, 3165, 10.1093/nar/gki627 Rangannan, 2007, Identification and annotation of promoter regions in microbial genome sequences on the basis of DNA stability, J Biosci, 32, 851 Akan, 2008, DNA sequence and structural properties as predictors of human and mouse promoters, Gene, 410, 165, 10.1016/j.gene.2007.12.011 de Avila e Silva, 2011, Rules extraction from neural networks applied to the prediction and recognition of prokaryotic promoters, Genet Mol Biol, 34, 353, 10.1590/S1415-47572011000200031 Breslauer, 1986, Predicting DNA duplex stability from the base sequence, Proc Natl Acad Sci USA, 83, 3746, 10.1073/pnas.83.11.3746 SantaLucia, 2004, The thermodynamics of DNA structural motifs, Annu Rev Biophys Biomol Struct, 33, 415, 10.1146/annurev.biophys.32.110601.141800 Gama-Castro, 2008, RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Text press navigation, Nucleic Acids Research, 36, D120, 10.1093/nar/gkm994 Kanhere, 2005, A novel method for prokaryotic promoter prediction based on DNA stability, BMC Bioinform, 6, 1471, 10.1186/1471-2105-6-1 Hegger, 1999, Practical implementation of nonlinear time series methods: the TISEAN package, CHAOS, 9, 413, 10.1063/1.166424 Battistella, 2004, The protein folding problem solved by a fuzzy inference system extracted from an artificial neural network, Lecture Notes Comput Sci, 3315, 474, 10.1007/978-3-540-30498-2_47 Tan, 2005, Predictive neural networks for gene expression data analysis, Neural Networks, 18, 297, 10.1016/j.neunet.2005.01.003 R Development Core Team, 2008 Sokolova, 2009, A systematic analysis of performance measures for classification tasks, Inform Process Manage, 427, 427, 10.1016/j.ipm.2009.03.002 Sonego, 2008, ROC analysis: applications to the classification of biological sequences and 3D structures, Brief Bioinform, 9, 198, 10.1093/bib/bbm064 Song, 2012, Recognition of prokaryotic promoters based on a novel variable-window Z-curve method, Nucleic Acids Res, 40, 963, 10.1093/nar/gkr795 Barrios, 1999, Compilation and analysis of σ54-dependent promoter sequences, Nucleic Acids Res, 27, 4305, 10.1093/nar/27.22.4305 Shingler, 2011, Signal sensory systems that impact σ54-dependent transcription, FEMS Microbiol Rev, 35, 425, 10.1111/j.1574-6976.2010.00255.x L. J. Friedman, J.Gelles, Mechanism of transcription initiation at an activator-dependent promoter defined by single-molecule observation, Cell 148(4) 679–689. Song, 2007, Sigma 28 promoter prediction in members of the gammaproteobacteria, FEMS, 271, 222, 10.1111/j.1574-6968.2007.00720.x Koo, 2009, Reduced capacity of alternative sigmas to melt promoters ensures stringent promoter recognition, Genes Dev, 23, 2426, 10.1101/gad.1843709 van Hijum, 2009, Mechanisms and evolution of control logic in prokaryotic transcriptional, Microbiol Mol Biol Rev, 73, 481, 10.1128/MMBR.00037-08 Huerta, 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals, J Mol Biol, 333, 261, 10.1016/j.jmb.2003.07.017