{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:34:27Z","timestamp":1767962067538,"version":"3.49.0"},"reference-count":75,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2009,2,11]],"date-time":"2009-02-11T00:00:00Z","timestamp":1234310400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,12]]},"DOI":"10.1186\/1471-2105-10-57","type":"journal-article","created":{"date-parts":[[2009,2,11]],"date-time":"2009-02-11T19:13:42Z","timestamp":1234379622000},"source":"Crossref","is-referenced-by-count":31,"title":["A reexamination of information theory-based methods for DNA-binding site identification"],"prefix":"10.1186","volume":"10","author":[{"given":"Ivan","family":"Erill","sequence":"first","affiliation":[]},{"given":"Michael C","family":"O'Neill","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,2,11]]},"reference":[{"key":"2787_CR1","first-page":"Unit 17.17","volume":"Chapter 17","author":"O Aparicio","year":"2004","unstructured":"Aparicio O, Geisberg JV, Struhl K: Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Current protocols in cell biology\/editorial board, Juan S Bonifacino [et al]. 2004, Chapter 17: Unit 17.17.","journal-title":"Current protocols in cell biology\/editorial board, Juan S Bonifacino [et al]"},{"issue":"8","key":"2787_CR2","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1038\/nmeth1068","volume":"4","author":"G Robertson","year":"2007","unstructured":"Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007, 4 (8): 651-657.","journal-title":"Nat Methods"},{"key":"2787_CR3","first-page":"28","volume":"2","author":"TL Bailey","year":"1994","unstructured":"Bailey TL, Elkan C: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf on Intell Syst Mol Biol. 1994, 2: 28-36.","journal-title":"Proc Int Conf on Intell Syst Mol Biol"},{"issue":"4","key":"2787_CR4","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1073\/pnas.86.4.1183","volume":"86","author":"GD Stormo","year":"1989","unstructured":"Stormo GD, Hartzell GW: Identifying protein-binding sites from unaligned DNA fragments. Proceedings of the National Academy of Sciences of the United States of America. 1989, 86 (4): 1183-1187.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"5131","key":"2787_CR5","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1126\/science.8211139","volume":"262","author":"CE Lawrence","year":"1993","unstructured":"Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC: Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science. 1993, 262 (5131): 208-214.","journal-title":"Science"},{"issue":"8","key":"2787_CR6","doi-asserted-by":"publisher","first-page":"1808","DOI":"10.1093\/nar\/28.8.1808","volume":"28","author":"J van Helden","year":"2000","unstructured":"van Helden J, Rios AF, Collado-Vides J: Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic acids research. 2000, 28 (8): 1808-1818.","journal-title":"Nucleic acids research"},{"issue":"1","key":"2787_CR7","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1186\/1471-2105-3-20","volume":"3","author":"D Betel","year":"2002","unstructured":"Betel D, Hogue C: Kangaroo \u2013 A pattern-matching program for biological sequences. BMC bioinformatics. 2002, 3 (1): 20.","journal-title":"BMC bioinformatics"},{"issue":"1","key":"2787_CR8","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1089\/cmb.1995.2.87","volume":"2","author":"MS Gelfand","year":"1995","unstructured":"Gelfand MS: Prediction of function in DNA sequence analysis. J Comput Biol. 1995, 2 (1): 87-115.","journal-title":"J Comput Biol"},{"issue":"18","key":"2787_CR9","doi-asserted-by":"publisher","first-page":"3516","DOI":"10.1093\/bioinformatics\/bth438","volume":"20","author":"R Osada","year":"2004","unstructured":"Osada R, Zaslavsky E, Singh M: Comparative analysis of methods for representing and searching for transcription factor binding sites. Bioinformatics (Oxford, England). 2004, 20 (18): 3516-3525.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"4","key":"2787_CR10","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1016\/0022-2836(87)90354-8","volume":"193","author":"OG Berg","year":"1987","unstructured":"Berg OG, von Hippel PH: Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. Journal of molecular biology. 1987, 193 (4): 723-750.","journal-title":"Journal of molecular biology"},{"issue":"6","key":"2787_CR11","doi-asserted-by":"publisher","first-page":"1608","DOI":"10.1073\/pnas.83.6.1608","volume":"83","author":"PH von Hippel","year":"1986","unstructured":"von Hippel PH, Berg OG: On the specificity of DNA-protein interactions. Proceedings of the National Academy of Sciences of the United States of America. 1986, 83 (6): 1608-1612.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"11","key":"2787_CR12","doi-asserted-by":"publisher","first-page":"5089","DOI":"10.1093\/nar\/16.11.5089","volume":"16","author":"OG Berg","year":"1988","unstructured":"Berg OG: Selection of DNA binding sites by regulatory proteins: the LexA protein and the arginine repressor use different strategies for functional specificity. Nucleic acids research. 1988, 16 (11): 5089-5105.","journal-title":"Nucleic acids research"},{"issue":"3","key":"2787_CR13","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1016\/0022-2836(86)90165-8","volume":"188","author":"TD Schneider","year":"1986","unstructured":"Schneider TD, Stormo GD, Gold L, Ehrenfeucht A: Information content of binding sites on nucleotide sequences. Journal of molecular biology. 1986, 188 (3): 415-431.","journal-title":"Journal of molecular biology"},{"key":"2787_CR14","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","volume":"27","author":"CE Shannon","year":"1948","unstructured":"Shannon CE: A mathematical theory of communication. Bell System Technical Journal. 1948, 27: 379-423.","journal-title":"Bell System Technical Journal"},{"issue":"2","key":"2787_CR15","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/0022-5193(66)90127-5","volume":"10","author":"LL Gatlin","year":"1966","unstructured":"Gatlin LL: The information content of DNA. J Theor Biol. 1966, 10 (2): 281-300.","journal-title":"J Theor Biol"},{"issue":"2","key":"2787_CR16","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1016\/0022-5193(68)90160-4","volume":"18","author":"LL Gatlin","year":"1968","unstructured":"Gatlin LL: The information content of DNA. II. J Theor Biol. 1968, 18 (2): 181-194.","journal-title":"J Theor Biol"},{"key":"2787_CR17","volume-title":"Elementary principles in statistical mechanics","author":"JW Gibbs","year":"1902","unstructured":"Gibbs JW: Elementary principles in statistical mechanics. 1902, New York: Charles Scribners Sons"},{"issue":"4","key":"2787_CR18","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1103\/PhysRev.106.620","volume":"106","author":"ET Jaynes","year":"1957","unstructured":"Jaynes ET: Information Theory and Statistical Mechanics. Physical Review. 1957, 106 (4): 620.","journal-title":"Physical Review"},{"issue":"2","key":"2787_CR19","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1103\/PhysRev.108.171","volume":"108","author":"ET Jaynes","year":"1957","unstructured":"Jaynes ET: Information Theory and Statistical Mechanics. II. Physical Review. 1957, 108 (2): 171.","journal-title":"Physical Review"},{"issue":"14","key":"2787_CR20","doi-asserted-by":"publisher","first-page":"2794","DOI":"10.1093\/nar\/28.14.2794","volume":"28","author":"TD Schneider","year":"2000","unstructured":"Schneider TD: Evolution of biological information. Nucleic acids research. 2000, 28 (14): 2794-2799.","journal-title":"Nucleic acids research"},{"key":"2787_CR21","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1214\/aoms\/1177729694","volume":"22","author":"S Kullback","year":"1951","unstructured":"Kullback S, Leibler RA: On information and sufficiency. Annals of Mathematical Statistics. 1951, 22: 79-86.","journal-title":"Annals of Mathematical Statistics"},{"issue":"1","key":"2787_CR22","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1006\/jtbi.1998.0785","volume":"195","author":"GD Stormo","year":"1998","unstructured":"Stormo GD: Information content and free energy in DNA\u2013protein interactions. J Theor Biol. 1998, 195 (1): 135-137.","journal-title":"J Theor Biol"},{"issue":"4","key":"2787_CR23","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1006\/jtbi.1997.0540","volume":"189","author":"TD Schneider","year":"1997","unstructured":"Schneider TD: Information Content of Individual Genetic Sequences. Journal of Theoretical Biology. 1997, 189 (4): 427-441.","journal-title":"Journal of Theoretical Biology"},{"issue":"1 Pt 2","key":"2787_CR24","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1093\/nar\/12.1Part2.505","volume":"12","author":"R Staden","year":"1984","unstructured":"Staden R: Computer methods to locate signals in nucleic acid sequences. Nucleic acids research. 1984, 12 (1 Pt 2): 505-519.","journal-title":"Nucleic acids research"},{"issue":"2","key":"2787_CR25","first-page":"81","volume":"6","author":"GZ Hertz","year":"1990","unstructured":"Hertz GZ, Hartzell GW, Stormo GD: Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci. 1990, 6 (2): 81-92.","journal-title":"Comput Appl Biosci"},{"issue":"3","key":"2787_CR26","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/S0968-0004(98)01187-6","volume":"23","author":"GD Stormo","year":"1998","unstructured":"Stormo GD, Fields DS: Specificity, free energy and information content in protein-DNA interactions. Trends in biochemical sciences. 1998, 23 (3): 109-113.","journal-title":"Trends in biochemical sciences"},{"issue":"2","key":"2787_CR27","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1016\/0022-2836(89)90256-8","volume":"207","author":"MC O'Neill","year":"1989","unstructured":"O'Neill MC: Consensus methods for finding and ranking DNA binding sites. Application to Escherichia coli promoters. Journal of molecular biology. 1989, 207 (2): 301-310.","journal-title":"Journal of molecular biology"},{"issue":"18","key":"2787_CR28","doi-asserted-by":"publisher","first-page":"10710","DOI":"10.1073\/pnas.95.18.10710","volume":"95","author":"MC O'Neill","year":"1998","unstructured":"O'Neill MC: A general procedure for locating and analyzing protein-binding sequence motifs in nucleic acids. Proceedings of the National Academy of Sciences of the United States of America. 1998, 95 (18): 10710-10715.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"2787_CR29","volume-title":"Proceedings of the seventh annual international conference on Research in computational molecular biology","author":"B Barash","year":"2003","unstructured":"Barash B, Elidan G, Friedman N, Kaplan T: Modeling dependencies in protein-DNA binding sites. Proceedings of the seventh annual international conference on Research in computational molecular biology. 2003, Berlin, Germany: ACM"},{"issue":"5","key":"2787_CR30","doi-asserted-by":"publisher","first-page":"1255","DOI":"10.1093\/nar\/30.5.1255","volume":"30","author":"ML Bulyk","year":"2002","unstructured":"Bulyk ML, Johnson PL, Church GM: Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic acids research. 2002, 30 (5): 1255-1261.","journal-title":"Nucleic acids research"},{"issue":"4","key":"2787_CR31","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1093\/clinchem\/39.4.561","volume":"39","author":"MH Zweig","year":"1993","unstructured":"Zweig MH, Campbell G: Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine. Clinical chemistry. 1993, 39 (4): 561-577.","journal-title":"Clinical chemistry"},{"issue":"5","key":"2787_CR32","first-page":"423","volume":"12","author":"EN Trifonov","year":"1996","unstructured":"Trifonov EN: Interfering contexts of regulatory sequence elements. Comput Appl Biosci. 1996, 12 (5): 423-429.","journal-title":"Comput Appl Biosci"},{"key":"2787_CR33","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1007\/0-387-29148-2_3","volume-title":"DNA Conformation and Transcription","author":"M Asayama","year":"2005","unstructured":"Asayama M, Ohyama T: Curved DNA and Prokaryotic Promoters. DNA Conformation and Transcription. 2005, 37-51."},{"issue":"23","key":"2787_CR34","doi-asserted-by":"publisher","first-page":"6770","DOI":"10.1093\/nar\/gkg882","volume":"31","author":"R Jauregui","year":"2003","unstructured":"Jauregui R, Abreu-Goodger C, Moreno-Hagelsieb G, Collado-Vides J, Merino E: Conservation of DNA curvature signals in regulatory regions of prokaryotic genes. Nucleic acids research. 2003, 31 (23): 6770-6777.","journal-title":"Nucleic acids research"},{"issue":"3","key":"2787_CR35","doi-asserted-by":"crossref","first-page":"361","DOI":"10.3233\/ISB-00139","volume":"4","author":"L Kozobay-Avraham","year":"2004","unstructured":"Kozobay-Avraham L, Hosid S, Bolshoy A: Curvature distribution in prokaryotic genomes. In silico biology. 2004, 4 (3): 361-375.","journal-title":"In silico biology"},{"issue":"16","key":"2787_CR36","doi-asserted-by":"publisher","first-page":"5275","DOI":"10.1093\/nar\/gkm471","volume":"35","author":"RK Shultzaberger","year":"2007","unstructured":"Shultzaberger RK, Roberts LR, Lyakhov IG, Sidorov IA, Stephen AG, Fisher RJ, Schneider TD: Correlation between binding rate constants and individual information of E. coli Fis binding sites. Nucleic acids research. 2007, 35 (16): 5275-5283.","journal-title":"Nucleic acids research"},{"issue":"4","key":"2787_CR37","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1006\/bbrc.2002.6559","volume":"291","author":"KL Griffith","year":"2002","unstructured":"Griffith KL, Shah IM, Myers TE, O'Neill MC, Wolf RE: Evidence for \"pre-recruitment\" as a new mechanism of transcription activation in Escherichia coli: the large excess of SoxS binding sites per cell relative to the number of SoxS molecules per cell. Biochem Biophys Res Commun. 2002, 291 (4): 979-986.","journal-title":"Biochem Biophys Res Commun"},{"issue":"10","key":"2787_CR38","doi-asserted-by":"publisher","first-page":"4919","DOI":"10.1073\/pnas.94.10.4919","volume":"94","author":"LJ Sun","year":"1997","unstructured":"Sun LJ, Peterson BR, Verdine GL: Dual role of the nuclear factor of activated T cells insert region in DNA recognition and cooperative contacts to activator protein 1. Proceedings of the National Academy of Sciences of the United States of America. 1997, 94 (10): 4919-4924.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"4","key":"2787_CR39","doi-asserted-by":"publisher","first-page":"1725","DOI":"10.1016\/S0006-3495(99)77334-0","volume":"76","author":"J Rudnick","year":"1999","unstructured":"Rudnick J, Bruinsma R: DNA-protein cooperative binding through variable-range elastic coupling. Biophysical journal. 1999, 76 (4): 1725-1733.","journal-title":"Biophysical journal"},{"issue":"7","key":"2787_CR40","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1093\/bioinformatics\/17.7.608","volume":"17","author":"D GuhaThakurta","year":"2001","unstructured":"GuhaThakurta D, Stormo GD: Identifying target sites for cooperatively binding factors. Bioinformatics (Oxford, England). 2001, 17 (7): 608-621.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"3","key":"2787_CR41","doi-asserted-by":"publisher","first-page":"771","DOI":"10.1093\/nar\/gkl956","volume":"35","author":"RK Shultzaberger","year":"2007","unstructured":"Shultzaberger RK, Chen Z, Lewis KA, Schneider TD: Anatomy of Escherichia coli sigma70 promoters. Nucleic acids research. 2007, 35 (3): 771-788.","journal-title":"Nucleic acids research"},{"issue":"1","key":"2787_CR42","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1006\/jmbi.2001.5040","volume":"313","author":"RK Shultzaberger","year":"2001","unstructured":"Shultzaberger RK, Bucheimer RE, Rudd KE, Schneider TD: Anatomy of Escherichia coli ribosome binding sites. Journal of molecular biology. 2001, 313 (1): 215-228.","journal-title":"Journal of molecular biology"},{"issue":"6","key":"2787_CR43","doi-asserted-by":"publisher","first-page":"2611","DOI":"10.1093\/nar\/15.6.2611","volume":"15","author":"GJ Phillips","year":"1987","unstructured":"Phillips GJ, Arnold J, Ivarie R: Mono- through hexanucleotide composition of the Escherichia coli genome: a Markov chain analysis. Nucleic acids research. 1987, 15 (6): 2611-2626.","journal-title":"Nucleic acids research"},{"issue":"2","key":"2787_CR44","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1101\/gr.335003","volume":"13","author":"DT Pride","year":"2003","unstructured":"Pride DT, Meinersmann RJ, Wassenaar TM, Blaser MJ: Evolutionary Implications of Microbial Genome Tetranucleotide Frequency Biases. Genome research. 2003, 13 (2): 145-158.","journal-title":"Genome research"},{"issue":"4","key":"2787_CR45","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1038\/nbt0406-423","volume":"24","author":"P D'Haeseleer","year":"2006","unstructured":"D'Haeseleer P: What are DNA sequence motifs?. Nature biotechnology. 2006, 24 (4): 423-425.","journal-title":"Nature biotechnology"},{"issue":"20","key":"2787_CR46","doi-asserted-by":"publisher","first-page":"6762","DOI":"10.1093\/nar\/gkm631","volume":"35","author":"Z Chen","year":"2007","unstructured":"Chen Z, Lewis KA, Shultzaberger RK, Lyakhov IG, Zheng M, Doan B, Storz G, Schneider TD: Discovery of Fur binding site clusters in Escherichia coli by information theory models. Nucleic acids research. 2007, 35 (20): 6762-6777.","journal-title":"Nucleic acids research"},{"issue":"4","key":"2787_CR47","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1006\/jtbi.2003.3153","volume":"220","author":"JT Kim","year":"2003","unstructured":"Kim JT, Martinetz T, Polani D: Bioinformatic principles underlying the information content of transcription factor binding sites. J Theor Biol. 2003, 220 (4): 529-544.","journal-title":"J Theor Biol"},{"issue":"4","key":"2787_CR48","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1016\/0300-9084(91)90109-E","volume":"73","author":"M Schnarr","year":"1991","unstructured":"Schnarr M, Oertel-Buchheit P, Kazmaier M, Granger-Schnarr M: DNA binding properties of the LexA repressor. Biochimie. 1991, 73 (4): 423-431.","journal-title":"Biochimie"},{"issue":"22","key":"2787_CR49","doi-asserted-by":"publisher","first-page":"7833","DOI":"10.1093\/nar\/11.22.7833","volume":"11","author":"A Kolb","year":"1983","unstructured":"Kolb A, Spassky A, Chapon C, Blazy B, Buc H: On the different binding affinities of CRP at the lac, gal and malT promoter regions. Nucleic acids research. 1983, 11 (22): 7833-7852.","journal-title":"Nucleic acids research"},{"issue":"2","key":"2787_CR50","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1042\/bj2610649","volume":"261","author":"K Gaston","year":"1989","unstructured":"Gaston K, Kolb A, Busby S: Binding of the Escherichia coli cyclic AMP receptor protein to DNA fragments containing consensus nucleotide sequences. The Biochemical journal. 1989, 261 (2): 649-653.","journal-title":"The Biochemical journal"},{"issue":"21","key":"2787_CR51","doi-asserted-by":"publisher","first-page":"5826","DOI":"10.1128\/JB.184.21.5826-5832.2002","volume":"184","author":"N Baichoo","year":"2002","unstructured":"Baichoo N, Helmann JD: Recognition of DNA by Fur: a Reinterpretation of the Fur Box Consensus Sequence. Journal of bacteriology. 2002, 184 (21): 5826-5832.","journal-title":"Journal of bacteriology"},{"issue":"2","key":"2787_CR52","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1016\/S0021-9258(19)84994-3","volume":"264","author":"PH von Hippel","year":"1989","unstructured":"von Hippel PH, Berg OG: Facilitated target location in biological systems. The Journal of biological chemistry. 1989, 264 (2): 675-678.","journal-title":"The Journal of biological chemistry"},{"issue":"6","key":"2787_CR53","doi-asserted-by":"publisher","first-page":"1560","DOI":"10.1046\/j.1365-2958.2000.01826.x","volume":"35","author":"AR Fernandez De Henestrosa","year":"2000","unstructured":"Fernandez De Henestrosa AR, Ogi T, Aoyagi S, Chafin D, Hayes JJ, Ohmori H, Woodgate R: Identification of additional genes belonging to the LexA regulon in Escherichia coli. Molecular microbiology. 2000, 35 (6): 1560-1572.","journal-title":"Molecular microbiology"},{"issue":"2","key":"2787_CR54","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1093\/nar\/17.2.659","volume":"17","author":"TD Schneider","year":"1989","unstructured":"Schneider TD, Stormo GD: Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique. Nucleic acids research. 1989, 17 (2): 659-674.","journal-title":"Nucleic acids research"},{"issue":"1","key":"2787_CR55","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1128\/JB.144.1.185-191.1980","volume":"144","author":"O Huisman","year":"1980","unstructured":"Huisman O, D'Ari R, George J: Further characterization of sfiA and sfiB mutations in Escherichia coli. Journal of bacteriology. 1980, 144 (1): 185-191.","journal-title":"Journal of bacteriology"},{"issue":"17","key":"2787_CR56","doi-asserted-by":"publisher","first-page":"2225","DOI":"10.1093\/bioinformatics\/btg303","volume":"19","author":"I Erill","year":"2003","unstructured":"Erill I, Escribano M, Campoy S, Barbe J: In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon. Bioinformatics (Oxford, England). 2003, 19 (17): 2225-2236.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"3","key":"2787_CR57","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1111\/j.1365-2958.2008.06423.x","volume":"70","author":"K Uchida","year":"2008","unstructured":"Uchida K, Furukohri A, Shinozaki Y, Mori T, Ogawara D, Kanaya S, Nohmi T, Maki H, Akiyama M: Overproduction of Escherichia coli DNA polymerase DinB (Pol IV) inhibits replication fork progression and is lethal. Mol Microbiol. 2008, 70 (3): 608-622.","journal-title":"Mol Microbiol"},{"issue":"3","key":"2787_CR58","doi-asserted-by":"publisher","first-page":"e41","DOI":"10.1371\/journal.pcbi.0030041","volume":"3","author":"S Krishna","year":"2007","unstructured":"Krishna S, Maslov S, Sneppen K: UV-induced mutagenesis in Escherichia coli SOS response: a quantitative model. PLoS computational biology. 2007, 3 (3): e41.","journal-title":"PLoS computational biology"},{"issue":"3","key":"2787_CR59","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1007\/BF00325901","volume":"189","author":"ST Cole","year":"1983","unstructured":"Cole ST: Characterisation of the promoter for the LexA regulated sulA gene of Escherichia coli. Mol Gen Genet. 1983, 189 (3): 400-404.","journal-title":"Mol Gen Genet"},{"issue":"1","key":"2787_CR60","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1007\/s00018-008-8378-6","volume":"66","author":"M Butala","year":"2008","unstructured":"Butala M, Zgur-Bertok D, Busby SJ: The bacterial LexA transcriptional repressor. Cell Mol Life Sci. 2008, 66 (1): 82-93.","journal-title":"Cell Mol Life Sci"},{"issue":"8\u20139","key":"2787_CR61","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1016\/S0300-9084(82)80088-6","volume":"64","author":"R Brent","year":"1982","unstructured":"Brent R: Regulation and autoregulation by lexA protein. Biochimie. 1982, 64 (8\u20139): 565-569.","journal-title":"Biochimie"},{"issue":"21","key":"2787_CR62","doi-asserted-by":"publisher","first-page":"11735","DOI":"10.1073\/pnas.96.21.11735","volume":"96","author":"JJ Kohler","year":"1999","unstructured":"Kohler JJ, Metallo SJ, Schneider TL, Schepartz A: DNA specificity enhanced by sequential binding of protein monomers. Proceedings of the National Academy of Sciences of the United States of America. 1999, 96 (21): 11735-11739.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"2","key":"2787_CR63","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1089\/10665270252935566","volume":"9","author":"G Thijs","year":"2002","unstructured":"Thijs G, Marchal K, Lescot M, Rombauts S, De Moor B, Rouze P, Moreau Y: A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol. 2002, 9 (2): 447-464.","journal-title":"J Comput Biol"},{"key":"2787_CR64","first-page":"127","volume-title":"Pacific Symposium on Biocomputing","author":"X Liu","year":"2001","unstructured":"Liu X, Brutlag DL, Liu JS: BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pacific Symposium on Biocomputing. 2001, 127-138."},{"issue":"1\u20132","key":"2787_CR65","first-page":"51","volume":"21","author":"TL Bailey","year":"1995","unstructured":"Bailey TL, Elkan C: Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization. Machine Learning. 1995, 21 (1\u20132): 51-80.","journal-title":"Machine Learning"},{"key":"2787_CR66","first-page":"188","volume":"2","author":"JM Heumann","year":"1994","unstructured":"Heumann JM, Lapedes AS, Stormo GD: Neural networks for determining protein specificity and multiple alignment of binding sites. Proc Int Conf Intell Syst Mol Biol. 1994, 2: 188-194.","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"2787_CR67","volume-title":"Proceedings of the eighth annual international conference on Resaerch in computational molecular biology","author":"Z Xiaoyue","year":"2004","unstructured":"Xiaoyue Z, Haiyan H, Terence PS: Finding short DNA motifs using permuted markov models. Proceedings of the eighth annual international conference on Resaerch in computational molecular biology. 2004, San Diego, California, USA: ACM"},{"issue":"6","key":"2787_CR68","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1016\/S0097-8485(00)00072-3","volume":"24","author":"RV Parbhane","year":"2000","unstructured":"Parbhane RV, Tambe SS, Kulkarni BD: ANN modeling of DNA sequences: new strategies using DNA shape code. Computers & chemistry. 2000, 24 (6): 699-711.","journal-title":"Computers & chemistry"},{"issue":"2","key":"2787_CR69","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1093\/nar\/19.2.313","volume":"19","author":"MC O'Neill","year":"1991","unstructured":"O'Neill MC: Training back-propagation neural networks to define and detect DNA-binding sites. Nucleic acids research. 1991, 19 (2): 313-318.","journal-title":"Nucleic acids research"},{"issue":"22","key":"2787_CR70","doi-asserted-by":"publisher","first-page":"4187","DOI":"10.1093\/bioinformatics\/bti635","volume":"21","author":"R Munch","year":"2005","unstructured":"Munch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D: Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics (Oxford, England). 2005, 21 (22): 4187-4189.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"4","key":"2787_CR71","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1016\/j.jmb.2005.01.012","volume":"347","author":"RJ Redfield","year":"2005","unstructured":"Redfield RJ, Cameron AD, Qian Q, Hinds J, Ali TR, Kroll JS, Langford PR: A novel CRP-dependent regulon controls expression of competence genes in Haemophilus influenzae. Journal of molecular biology. 2005, 347 (4): 735-747.","journal-title":"Journal of molecular biology"},{"issue":"24","key":"2787_CR72","doi-asserted-by":"publisher","first-page":"8855","DOI":"10.1128\/JB.01213-07","volume":"189","author":"M Abella","year":"2007","unstructured":"Abella M, Campoy S, Erill I, Rojo F, Barbe J: Cohabitation of two different lexA regulons in Pseudomonas putida. Journal of bacteriology. 2007, 189 (24): 8855-8862.","journal-title":"Journal of bacteriology"},{"issue":"1","key":"2787_CR73","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1093\/nar\/gkg037","volume":"31","author":"R Munch","year":"2003","unstructured":"Munch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E, Jahn D: PRODORIC: prokaryotic database of gene regulation. Nucleic acids research. 2003, 31 (1): 266-269.","journal-title":"Nucleic acids research"},{"issue":"20","key":"2787_CR74","doi-asserted-by":"publisher","first-page":"6097","DOI":"10.1093\/nar\/18.20.6097","volume":"18","author":"TD Schneider","year":"1990","unstructured":"Schneider TD, Stephens RM: Sequence logos: a new way to display consensus sequences. Nucleic acids research. 1990, 18 (20): 6097-6100.","journal-title":"Nucleic acids research"},{"issue":"6","key":"2787_CR75","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1101\/gr.849004","volume":"14","author":"GE Crooks","year":"2004","unstructured":"Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: a sequence logo generator. Genome research. 2004, 14 (6): 1188-1190.","journal-title":"Genome research"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-57.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-10-57\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-57.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,7]],"date-time":"2025-02-07T16:47:57Z","timestamp":1738946877000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-57"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,2,11]]},"references-count":75,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["2787"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-57","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,2,11]]},"article-number":"57"}}