{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,3,22]],"date-time":"2024-03-22T11:11:38Z","timestamp":1711105898272},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"S17","license":[{"start":{"date-parts":[[2012,12,1]],"date-time":"2012-12-01T00:00:00Z","timestamp":1354320000000},"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":[[2012,12]]},"DOI":"10.1186\/1471-2105-13-s17-s10","type":"journal-article","created":{"date-parts":[[2012,12,13]],"date-time":"2012-12-13T06:16:01Z","timestamp":1355379361000},"source":"Crossref","is-referenced-by-count":14,"title":["A hybrid method for the exact planted (l, d) motif finding problem and its parallelization"],"prefix":"10.1186","volume":"13","author":[{"given":"Mostafa M","family":"Abbas","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohamed","family":"Abouelhoda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hazem M","family":"Bahig","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,12,13]]},"reference":[{"issue":"4","key":"5474_CR1","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1007\/BF02459500","volume":"46","author":"MS Waterman","year":"1984","unstructured":"Waterman MS, Aratia R, Galas DJ: Pattern recognition in several sequences: consensus and alignment. Bulletin of Mathematical Biology. 1984, 46 (4): 515-527.","journal-title":"Bulletin of Mathematical Biology"},{"key":"5474_CR2","first-page":"269","volume-title":"Proceedings of Eighth International Conference on Intelligent Systems for Molecular Biology","author":"P Pevzner","year":"2000","unstructured":"Pevzner P, Sze SH: Combinatorial approaches to finding subtle signals in DNA sequences. Proceedings of Eighth International Conference on Intelligent Systems for Molecular Biology. 2000, 269-278."},{"key":"5474_CR3","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1002\/prot.340070105","volume":"7","author":"C Lawrence","year":"1990","unstructured":"Lawrence C, Reilly A: An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins: Structure, Function and Genetics. 1990, 7: 41-51. 10.1002\/prot.340070105.","journal-title":"Proteins: Structure, Function and Genetics"},{"key":"5474_CR4","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1126\/science.8211139","volume":"262","author":"C Lawrence","year":"1993","unstructured":"Lawrence C, Altschul S, Boguski M, Liu J, Neuwald A, Wootton J: Detecting subtle sequence signals: A Gibbs Sampling strategy for multiple alignment. Science. 1993, 262: 208-214. 10.1126\/science.8211139.","journal-title":"Science"},{"key":"5474_CR5","first-page":"51","volume":"21","author":"T Bailey","year":"1995","unstructured":"Bailey T, Elkan C: Unsupervised learning of multiple motifs in biopolymers using Expectation Maximization. Machine Learning. 1995, 21: 51-80.","journal-title":"Machine Learning"},{"key":"5474_CR6","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1093\/bioinformatics\/11.4.379","volume":"11","author":"Y Fraenkel","year":"1995","unstructured":"Fraenkel Y, Mandel Y, Friedberg D, Margalit H: Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon. Bioinformatics. 1995, 11: 379-387. 10.1093\/bioinformatics\/11.4.379.","journal-title":"Bioinformatics"},{"key":"5474_CR7","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1093\/bioinformatics\/14.1.55","volume":"14","author":"I Rigoutsos","year":"1998","unstructured":"Rigoutsos I, Floratos A: Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics. 1998, 14: 55-67. 10.1093\/bioinformatics\/14.1.55.","journal-title":"Bioinformatics"},{"key":"5474_CR8","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1093\/bioinformatics\/15.7.563","volume":"15","author":"GZ Hertz","year":"1999","unstructured":"Hertz GZ, Stormo GD: Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics. 1999, 15: 563-577. 10.1093\/bioinformatics\/15.7.563.","journal-title":"Bioinformatics"},{"key":"5474_CR9","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1093\/nar\/28.3.695","volume":"28","author":"M Gelfand","year":"2000","unstructured":"Gelfand M, Koonin E, Mironov A: Prediction of transcription regulatory sites in archaea by a comparative genomic approach. Nucleic Acid Res. 2000, 28: 695-705. 10.1093\/nar\/28.3.695.","journal-title":"Nucleic Acid Res"},{"issue":"2","key":"5474_CR10","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1089\/10665270252935430","volume":"9","author":"J Buhler","year":"2002","unstructured":"Buhler J, Tompa M: Finding motifs using random projections. Journal of Computational Biology. 2002, 9 (2): 225-242. 10.1089\/10665270252935430.","journal-title":"Journal of Computational Biology"},{"issue":"2","key":"5474_CR11","doi-asserted-by":"publisher","first-page":"ii149","DOI":"10.1093\/bioinformatics\/btg1072","volume":"19","author":"A Price","year":"2003","unstructured":"Price A, Ramabhadran S, Pevzner PA: Finding subtle motifs by branching from sample strings. Bioinformatics. 2003, 19 (2): ii149-ii155. 10.1093\/bioinformatics\/btg1072.","journal-title":"Bioinformatics"},{"issue":"4","key":"5474_CR12","doi-asserted-by":"publisher","first-page":"959","DOI":"10.1109\/TCBB.2010.92","volume":"8","author":"C Huang","year":"2011","unstructured":"Huang C, Lee W, Hsieh S: An improved heuristic algorithm for finding motif signals in DNA sequences. IEEE\/ACM Transactions on Computational Biology and Bioinformatics. 2011, 8 (4): 959-975.","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"issue":"1","key":"5474_CR13","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1016\/0022-2836(85)90262-1","volume":"186","author":"DJ Galas","year":"1985","unstructured":"Galas DJ, Eggert M, Waterman MS: Rigorous pattern-recognition methods for DNA sequences: analysis of promoter sequences from Escherichia coli. Journal of Molecular Biology. 1985, 186 (1): 117-128. 10.1016\/0022-2836(85)90262-1.","journal-title":"Journal of Molecular Biology"},{"issue":"4","key":"5474_CR14","first-page":"293","volume":"5","author":"R Staden","year":"1989","unstructured":"Staden R: Methods for discovering novel motifs in nucleic acid sequences. Computer Applications in the Biosciences. 1989, 5 (4): 293-298.","journal-title":"Computer Applications in the Biosciences"},{"key":"5474_CR15","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1101\/gr.8.11.1202","volume":"15","author":"A Brazma","year":"1998","unstructured":"Brazma A, Jonassen I, Vilo J, Ukkonen E: Predicting gene regulatory elements in silico on a genomic scale. Genome Research. 1998, 15: 1202-1215.","journal-title":"Genome Research"},{"key":"5474_CR16","first-page":"111","volume-title":"Latin'98: Theoretical informatics, LNCS","author":"MF Sagot","year":"1998","unstructured":"Sagot MF: Spelling approximate repeated or common motifs using a suffix tree. Latin'98: Theoretical informatics, LNCS. Edited by: Lucchesi CL, Moura AV. 1998, 1380: 111-127."},{"issue":"5","key":"5474_CR17","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1006\/jmbi.1998.1947","volume":"281","author":"J Van Helden","year":"1998","unstructured":"Van Helden J, Andre B, Collado-Vides J: Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. Journal of Molecular Biology. 1998, 281 (5): 827-842. 10.1006\/jmbi.1998.1947.","journal-title":"Journal of Molecular Biology"},{"key":"5474_CR18","first-page":"262","volume-title":"Proceedings of seventh International Conference on Intelligent Systems for Molecular Biology","author":"M Tompa","year":"1999","unstructured":"Tompa M: An exact method for finding short motifs in sequences with application to the ribosome binding site problem. Proceedings of seventh International Conference on Intelligent Systems for Molecular Biology. 1999, 262-271."},{"issue":"3-4","key":"5474_CR19","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1089\/106652700750050826","volume":"7","author":"L Marsan","year":"2000","unstructured":"Marsan L, Sagot MF: Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. Journal of Computational Biology. 2000, 7 (3-4): 345-362. 10.1089\/106652700750050826.","journal-title":"Journal of Computational Biology"},{"key":"5474_CR20","first-page":"344","volume-title":"Proceedings of Eighth International Conference on Intelligent Systems for Molecular Biology","author":"S Sinha","year":"2000","unstructured":"Sinha S, Tompa M: A statistical method for finding transcription factor binding sites. Proceedings of Eighth International Conference on Intelligent Systems for Molecular Biology. 2000, 344-354."},{"key":"5474_CR21","volume-title":"Proceedings of Fifth International Conference Computational Biology (RECOMB 2001)","author":"M Blanchette","year":"2001","unstructured":"Blanchette M: Algorithms for phylogenetic footprinting. Proceedings of Fifth International Conference Computational Biology (RECOMB 2001). 2001"},{"issue":"1","key":"5474_CR22","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1093\/bioinformatics\/18.suppl_1.S354","volume":"18","author":"E Eskin","year":"2002","unstructured":"Eskin E, Pevzner PA: Finding composite regulatory patterns in DNA sequences. Bioinformatics. 2002, 18 (1): 354-363. 10.1093\/bioinformatics\/18.suppl_1.S354.","journal-title":"Bioinformatics"},{"key":"5474_CR23","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/978-3-540-45078-8_5","volume-title":"Proceedings of Eighth International Workshop Algorithms and Data Structures (WADS03)","author":"PA Evans","year":"2003","unstructured":"Evans PA, Smith A: Toward optimal motif enumeration. Proceedings of Eighth International Workshop Algorithms and Data Structures (WADS03). 2003, 47-58."},{"key":"5474_CR24","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1142\/9781860947322_0027","volume-title":"Proceedings of Third Asia Pacific Bioinformatics Conference","author":"AM Carvalho","year":"2005","unstructured":"Carvalho AM, Freitas AT, Oliveira AL, Sagot MF: A highly scalable algorithm for the extraction of CIS-Regulatory regions. Proceedings of Third Asia Pacific Bioinformatics Conference. 2005, 273-282."},{"key":"5474_CR25","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1142\/9781860947322_0026","volume-title":"Proceedings of Third Asia Pacific Bioinformatics Conference","author":"FYL Chin","year":"2005","unstructured":"Chin FYL, Leung HCM: Voting algorithms for discovering long motifs. Proceedings of Third Asia Pacific Bioinformatics Conference. 2005, 261-271."},{"issue":"8","key":"5474_CR26","doi-asserted-by":"publisher","first-page":"1117","DOI":"10.1089\/cmb.2005.12.1117","volume":"12","author":"S Rajasekaran","year":"2005","unstructured":"Rajasekaran S, Balla S, Huang C-H: Exact algorithms for planted motif problems. Journal of Computational Biology. 2005, 12 (8): 1117-1128. 10.1089\/cmb.2005.12.1117.","journal-title":"Journal of Computational Biology"},{"key":"5474_CR27","first-page":"822","volume-title":"Proceedings of Second International Workshop on Bioinformatics Research and Applications (LNCS 3992)","author":"J Davila","year":"2006","unstructured":"Davila J, Balla S, Rajasekaran S: Space and time efficient algorithms for planted motif search. Proceedings of Second International Workshop on Bioinformatics Research and Applications (LNCS 3992). 2006, 822-829."},{"key":"5474_CR28","first-page":"757","volume-title":"Proceedings of Seventh Latin American Theoretical Informatics Symposium","author":"N Pisanti","year":"2006","unstructured":"Pisanti N, Carvalho A, Marsan L, Sagot MF: RISOTTO: fast extraction of motifs with mismatches. Proceedings of Seventh Latin American Theoretical Informatics Symposium. 2006, 757-768."},{"key":"5474_CR29","first-page":"544","volume-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics","author":"J Davila","year":"2007","unstructured":"Davila J, Balla S, Rajasekaran S: Fastand practical algorithms for planted (l, d) motif search. IEEE\/ACM Transactions on Computational Biology and Bioinformatics. 2007, 544-552."},{"key":"5474_CR30","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1186\/1471-2105-12-410","volume":"12","author":"H Dinh","year":"2011","unstructured":"Dinh H, Rajasekaran S, Kundeti V: PMS5: an efficient exact algorithm for the (l, d)-motif finding problem. BMC Bioinformatics. 2011, 12: 410-420. 10.1186\/1471-2105-12-410.","journal-title":"BMC Bioinformatics"},{"key":"5474_CR31","first-page":"1108.5217","volume-title":"CoRR abs","author":"D Sharma","year":"2011","unstructured":"Sharma D, Rajasekaran S, Dinh H: An experimental comparison of PMSprune and other algorithms for motif search. CoRR abs. 2011, 1108.5217-"},{"key":"5474_CR32","first-page":"725","volume-title":"Proceedings of Seventh ACS\/IEEE International Conference on Computer Systems and Applications","author":"MM Abbas","year":"2009","unstructured":"Abbas MM, Bahig HM: Performance and analysis of modified voting algorithm for planted motif search. Proceedings of Seventh ACS\/IEEE International Conference on Computer Systems and Applications. 2009, 725-731."},{"key":"5474_CR33","first-page":"65","volume-title":"Experimental Medicine and Biology, special issue Advanced in Computational Biology, Springer","author":"HM Bahig","year":"2010","unstructured":"Bahig HM, Abbas MM, Bhery A: Experimental study of modified voting algorithm for planted (l, d)-motif problem. Experimental Medicine and Biology, special issue Advanced in Computational Biology, Springer. 2010, 65-73."},{"key":"5474_CR34","doi-asserted-by":"crossref","unstructured":"Rajasekaran S, Dinh H: A speedup technique for (l, d)-motif finding algorithms. BMC Research Notes. 2011, 54-61. 4","DOI":"10.1186\/1756-0500-4-54"},{"key":"5474_CR35","volume-title":"Cambridge university Press, New York","author":"D Gusfield","year":"1977","unstructured":"Gusfield D: Algorithms on strings, trees, and sequences: computer science and computational biology. Cambridge university Press, New York. 1977"},{"issue":"5","key":"5474_CR36","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1101\/gr.6902","volume":"12","author":"J Blanchette","year":"2002","unstructured":"Blanchette J, Tompa M: Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Research. 2002, 12 (5): 739-748. 10.1101\/gr.6902.","journal-title":"Genome Research"},{"key":"5474_CR37","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1093\/nar\/26.1.73","volume":"26","author":"JM Cherry","year":"1998","unstructured":"Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D: SGD: Saccharomyces Genome Database. Nucleic Acid Res. 1998, 26: 73-79. 10.1093\/nar\/26.1.73. [ http:\/\/www.yeastgenome.org\/ ]","journal-title":"Nucleic Acid Res"},{"issue":"7-8","key":"5474_CR38","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1093\/bioinformatics\/15.7.607","volume":"15","author":"J Zhu","year":"1999","unstructured":"Zhu J, Zhang M: SCPD: A Promoter Database of the Yeast Saccha-Romyces Cerevisiae. Bioinformatics. 1999, 15 (7-8): 607-611. [ http:\/\/cgsigma.cshl.org\/jian\/ ]","journal-title":"Bioinformatics"},{"issue":"10","key":"5474_CR39","doi-asserted-by":"publisher","first-page":"1277","DOI":"10.1101\/gad.11.10.1277","volume":"11","author":"CJ McInerny","year":"1997","unstructured":"McInerny CJ, Partridge JF, Mikesell GE, Creemer DP, Breeden LL: A novel Mcm1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M\/G1-specific transcription. Genes Dev. 1997, 11 (10): 1277-1288. 10.1101\/gad.11.10.1277.","journal-title":"Genes Dev"},{"issue":"1","key":"5474_CR40","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1093\/nar\/24.1.238","volume":"24","author":"E Wingender","year":"1996","unstructured":"Wingender E, Dietze P, Karas H, Knuppel R: TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Research. 1996, 24 (1): 238-241. 10.1093\/nar\/24.1.238. [ http:\/\/transfac.gbf-braunschweig.de\/TRANSFAC\/ ]","journal-title":"Nucleic Acids Research"},{"issue":"11","key":"5474_CR41","doi-asserted-by":"publisher","first-page":"5975","DOI":"10.1128\/MCB.15.11.5975","volume":"15","author":"S Natesan","year":"1995","unstructured":"Natesan S, Gilman M: YY1 facilitates the association of serum response factor with the c-fos serum response element. Mol Cell Biol. 1995, 15 (11): 5975-5982.","journal-title":"Mol Cell Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S17-S10.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-13-S17-S10\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S17-S10.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,7,6]],"date-time":"2019-07-06T21:29:48Z","timestamp":1562448588000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-S17-S10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,12]]},"references-count":41,"journal-issue":{"issue":"S17","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["5474"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-s17-s10","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,12]]},"article-number":"S10"}}