iTriplet, a rule-based nucleic acid sequence motif finder

Algorithms for Molecular Biology

Volumn 4, Issue 1, 2009, Pages

  Ho, Eric S ^a   Jakubowski, Christopher D ^a   Gunderson, Samuel I ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 71049179049     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-4-14     Document Type: Article

References (37)

1. Pevzner PA, Sze SH. Combinatorial approaches to finding subtle signals in DNA sequences. Proc Int Conf Intell Syst Mol Biol 2000, 8:269-78.
2. Das MK, Dai HK. A survey of DNA motif finding algorithms. BMC Bioinformatics 2007, 8(Suppl 7):S21. 2099490, 18047721.
3. Rajasekaran S. Algorithms for motif search. Handbook of Computational Biology 2006, 37:1-21. Chapman & Hall/CRC, Srinivas Aluru.
4. Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology 1994, 28-36.
5. Bailey TL, Elkan C. Unsupervised Learning of Multiple Motifs in Biopolymers using EM. Machine Learning 1995, 21(1-2):51-80.
6. Roth FP, Hughes JD, Estep PW, Church GM. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnology 1998, 10:939-45.
7. Liu X, Brutlag DL, Liu JS. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 2001, 6:127-38.
8. Liu X, Brutlag DL, Liu JS. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nature Biotechnology 2002, 20:835-9.
9. Thijs G, Marchal K, Lescot M, Rombauts S, De Moor B, Rouzé P, Moreau Y. A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. Journal of Computational Biology 2002, 9:447-64.
10. Blanchette M, Tompa M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Research 2002, 5:739-48.
11. Siddharthan R, Siggia ED, van Nimwegen E. PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Computational Biology 2005, 7:e67.
12. Wang J, Hannenhalli S. Generalizations of Markov model to characterize biological sequences. BMC Bioinformatics 2005, 6:219. 1236913, 16144548.
13. Sze SH, Zhao X. Improved pattern-driven algorithms for motif finding in DNA sequences. Proceedings of the 2005 Joint RECOMB Satellite Workshops on Systems Biology and Regulatory Genomics. Lecture Notes in Bioinformatics 2006, 4023:198-211.
14. Eskin E, Pevzner PA. Finding composite regulatory patterns in DNA sequences. Bioinformatics 2002, 18(Suppl 1):S354-63.
15. Rigoutsos I, Floratos A. Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics 1998, 14(1):55-67.
16. Jensen KL, Styczynski MP, Rigoutsos I, Stephanopoulos GN. A generic motif discovery algorithm for sequential data. Bioinformatics 2006, 22(1):21-8.
17. Davila J, Balla S, Rajasekaran S. Fast and practical algorithms for planted (l, d) motif search. IEEE/ACM Trans Computational Biology & Bioinformatics 2007, 4:544-52.
18. Pisanti N, Carvalho AM, Marsan L, Oliveira AL, Sagot MF. RISOTTO: Fast extraction of motifs with mismatches. Proceedings of the 7th Latin American Theoretical Informatics Symposium 2006, 3887:757-768.
19. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A sequence logo generator. Genome Research 2004, 14:1188-1190. 419797, 15173120.
20. Salgado H, Gama-Castro S, Martinez-Antonio A, Diaz-Peredo E, Sanchez-Solano F, Peralta-Gil M, Garcia-Alonso D, Jimenez-Jacinto V, Santos-Zavaleta A, Bonavides-Martinez C, Cllado-Vides J. RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Research 2004, 32:D303-306. 308874, 14681419.
21. Hu J, Li B, Kihara D. Limitations and potentials of current motif discovery algorithms. Nucleic Acids Research 2005, 33(15):4899-913. 1199555, 16284194.
22. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology 2005, 23(1):137-44.
23. Pavesi G, Mereghetti P, Mauri G, Pesole G. Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Research 2004, (32 Web Server):W199-203. 441603, 15215380.
24. Tian B, Hu J, Zhang H, Lutz CS. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Research 2005, 33(1):201-12. 546146, 15647503.
25. Zhao J, Hyman L, Moore C. Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev 1999, 63(2):405-45. 98971, 10357856.
26. Salisbury J, Hutchison KW, Graber JH. A multispecies comparison of the metazoan 3'-processing downstream elements and the CstF-64 RNA recognition motif. BMC Genomics 2006, 7(1):55. 1539018, 16542450.
27. Chen F, Wilusz J. Auxiliary downstream elements are required for efficient polyadenylation of mammalian pre-mRNAs. Nucleic Acids Research 1998, 26(12):2891-8. 147640, 9611233.
28. Perez Canadillas JM, Varani G. Recognition of GU-rich polyadenylation regulatory elements by human CstF-64 protein. EMBO J 2003, 22(11):2821-30. 156756, 12773396.
29. Kent WJ. BLAT - The BLAST-Like Alignment Tool. Genome Research 2002, 12(4):656-664. 187518, 11932250.
30. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The Human Genome Browser at UCSC. Genome Research 2002, 12(6):996-1006. 186604, 12045153.
31. Piqué M, López JM, Foissac S, Guigó R, Méndez R. A combinatorial code for CPE-mediated translational control. Cell 2008, 132(3):434-48.
32. Chen CY, Shyu AB. AU-rich elements: characterization and importance in mRNA degradation. Trends Biochem Sci 1995, 11:465-70.
33. Bakheet T, Frevel M, Williams BR, Greer W, Khabar KS. ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins. Nucleic Acids Research 2001, 1:246-54.
34. Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research 2007, (35 Database):D61-5. 1716718, 17130148.
35. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ. The UCSC Genome Browser Database. Nucleic Acids Research 2003, 31(1):51-54. 165576, 12519945.
36. Goraczniak R, Gunderson SI. The regulatory element in the 3'-untranslated region of human papillomavirus 16 inhibits expression by binding CUG-binding protein 1. J Biol Chem 2008, 283(4):2286-96. 18042543.
37. Wingender E, Dietze P, Karas H, Knüppel R. TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Research 1996, 24(1):238-41. 145586, 8594589.