A combinatorial optimization approach for diverse motif finding applications

Algorithms for Molecular Biology

Volumn 1, Issue 1, 2006, Pages

  Zaslavsky, Elena ^a   Singh, Mona ^a  

^a Princeton University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 34248380020     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-1-13     Document Type: Article

References (47)

1. Tompa M Li N Bailey TL Church G De Moor B Eskin E Favorov AV Frith M Fu Y Kent WJ Makeev VJ Mironov AA Noble WS Pavesi G Pesole G Regnier 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 Nat Biotechnol 2005 23 1 137-144 15637633
2. Hu J Li B Kihara D Limitations and potentials of current motif discovery algorithms Nucleic Acids Res 2005 33 15 4899-4913 1199555 16284194
3. Tavazoie S Hughes JD Campbell MJ Cho RJ Church G Systematic determination of genetic network architecture Nature Genetics 1999 22 3 281-285 10391217
4. Lee T Rinaldi N Robert F Odom D Bar-Joseph Z Gerber G Hannett N Harbison C Thompson C Simon I Zeitlinger J Jennings E Murray H Gordon D Ren B Wyrick J Tagne J Volkert T Fraenkel E Gifford D Young R Transcriptional regulatory networks in Saccharomyces cerevisiae Science 2002 298 5594 799-804 12399584
5. Mukherjee S Berger M Jona G Wang X Muzzey D Snyder M Young R Bulyk M Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays Nature Genetics 2004 36 12 1331-1339 15543148
6. McGuire A Hughes J Church G Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes Genome Res 2000 10 6 744-757 10854408
7. Cliften P Sundarsanam P Desikan A Fulton L Fulton B Majors J Waterston R Cohen B Johnston M Finding functional features in Saccharomyces genomes by phylogenetic footprinting Science 2003 301 5629 71-76 12775844
8. McCue L Thompson W Carmack C Ryan M Liu J Derbyshire V Lawrence C Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes Nucleic Acids Res 2001 29 3 774-782 30389 11160901
9. Blanchette M Tompa M Discovery of regulatory elements by a computational method for phylogenetic footprinting Genome Res 2002 12 739-748 186562 11997340
10. Kellis M Patterson N Endrizzi M Birren B Lander E Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 2003 423 241-254 12748633
11. Dayhoff M Schwartz R Orcutt B A model of evolutionary change in proteins Atlas of Protein Sequence and Structure Silver Spring, MD: National Biomedical Research Foundation Dayhoff M 1978 5 3 345-352
12. Henikoff S Henikoff J Amino acid substitution matrices from protein blocks Proc Natl Acad Sci USA 1992 89 10915-10919 50453 1438297
13. Hon LS Jain AN A deterministic motif finding algorithm with application to the human genome Bioinformatics 2006 22 9 1047-1054 16455748
14. Lawrence C Reilly A An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences Proteins 1990 7 41-51 2184437
15. 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 8211139
16. Liu X Brutlag D Liu J BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes Pac Symp Biocomput 2001 127-138 11262934
17. Pevzner P Sze S Combinatorial approaches to finding subtle signals in DNA sequences Proc Int Conf Intell Syst Mol Biol 2000 8 269-278 10977088
18. Bailey T Elkan C Unsupervised learning of multiple motifs in biopolymers using expectation maximization Machine Learning 1995 21 51-80
19. Hertz G Stormo G Identifying DNA and protein patterns with statistically significant alignments of multiple sequences Bioinformatics 1999 15 563-577 10487864
20. Marsan L Sagot MF Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification J Comput Biol 2000 7 345-362 11108467
21. Hughes J Estep P Tavazoie S Church G Computational identification of cis-regulatory elements associated with groups of functionally related genes in S. cerevisiae J Mol Biol 2000 296 1205-1214 10698627
22. Buhler J Tompa M Finding motifs using random projections J Comput Biol 2002 9 2 225-242 12015879
23. Sinha S Tompa M A program for discovery of novel transcription factor binding sites by statistical overrepresentation Nucleic Acids Res 2003 31 13 3586-3588 169024 12824371
24. 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 Res 2004 32 W199-W203 441603 15215380
25. Stormo GD DNA binding sites: Representation and discovery Bioinformatics 2000 16 16-23 10812473
26. Li N Tompa M Analysis of computational approaches for motif discovery Algorithms for Molecular Biology 2006 1 8 1540429 16722558
27. Akutsu T Arimura H Shimozono S On approximation algorithms for local multiple alignment Proceedings of the Fourth Annual International Conference on Research in Computational Molecular Biology ACM Press 2000 1-7
28. Robison K McGuire AM Church GM A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 Genome J Mol Biol 1998 284 241-254 9813115
29. Boeckmann B Bairoch A Apweiler R Blatter MC Estreicher A Gasteiger E Martin M Michoud K O'Donovan C Phan I Pilbout S Schneider M The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucleic Acids Res 2003 31 365-370 165542 12520024
30. Carillo H Lipman D The multiple sequence alignment problem in biology SIAM Journal on Applied Math 1988 48 1073-1082
31. Schuler G Altschul S Lipman D A workbench for multiple alignment construction and analysis Proteins 1991 9 3 180-190 2006136
32. Osada R Zaslavsky E Singh M Comparative analysis of methods for representing and searching for transcription factor binding sites Bioinformatics 2004 20 18 3516-3525 15297295
33. Man TK Stormo GD Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay Nucl Acids Res 2001 29 2471-2478 55749 11410653
34. Bulyk ML Johnson PL Church GM Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors Nucl Acids Res 2002 30 5 1255-1261 101241 11861919
35. Gusfield D Efficient methods for multiple sequence alignment with guaranteed error bounds Bull Math Biol 1993 55 1 141-154 7680269
36. Lukashin A Rosa J Local multiple sequence alignment using dead-end elimination Bioinformatics 1999 15 947-953 10743561
37. Desmet J De Maeyer M Hazes B Lasters I The dead-end elimination theorem and its use in protein side-chain positioning Nature 1992 356 539-542
38. Tatusov R Altschul S Koonin E Detection of Conserved Segments in Proteins: Iterative Scanning of Sequence Databases With Alignment Blocks Proc Natl Acad Sci USA 1994 91 12091-12095 45382 7991589
39. Thompson W Rouchka EC Lawrence CE Gibbs Recursive Sampler: Finding transcription factor binding sites Nucleic Acids Res 2003 31 13 3580-3585 169014 12824370
40. Vingron M Pevzner P Multiple sequence comparison and consistency on multipartite graphs Advances in Applied Mathematics 1995 16 1-22
41. Kingsford C Chazelle B Singh M Solving and analyzing side-chain positioning problems using linear and integer programming Bioinformatics 2005 21 7 1028-1039 15546935
42. Feng D Doolittle RF Progressive sequence alignment as a prerequisite to correct phylogenetic trees J Mol Evol 1987 25 4 351-360 3118049
43. Neuwald A Liu J Lawrence C Gibbs motif sampling: Detection of bacterial outer membrane protein repeats Protein Sci 1995 4 8 1618-32 8520488
44. Schneider TD Stormo CD Gold L Ehrenfeucht A Information content of binding sites on nucleotide sequences J Mol Biol 1986 188 415-431 3525846
45. Wingender E Dietze P Karas H Knüppel R TRANSFAC: A database on transcription factors and their DNA binding sites Nucleic Acids Res 1996 24 238-241 145586 8594589
46. Prakash A Tompa M Statistics of local multiple alignments Bioinformatics 2005 21 i344-i350 15961477
47. Kingsford C Zaslavsky E Singh M A compact mathematical programming formulation for DNA motif finding Proceedings of the Seventeenth Annual Symposium on Combinatorial Pattern Matching (CPM), Barcelona, Spain Springer 2006 233-245