A survey of DNA motif finding algorithms

BMC Bioinformatics

Volumn 8, Issue SUPPL. 7, 2007, Pages

  Das, Modan K ^a,b   Dai, Ho Kwok ^a  

^a Department of Computer Science   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SCIENTISTS; EXPERIMENTAL APPROACHES; GENE EXPRESSION ANALYSIS; INTEGRATED APPROACH; MOTIF FINDING ALGORITHMS; ORTHOLOGOUS SEQUENCES; PERFORMANCE COMPARISON; REGULATORY MECHANISM;

ALGORITHMS; BINDING SITES; BIOLOGY; DNA; GENE EXPRESSION; SURVEYS; TOOLS;

MATHEMATICAL MODELS;

DNA; TRANSCRIPTION FACTOR;

CONFERENCE PAPER; CONTROLLED STUDY; DNA DETERMINATION; DNA FOOTPRINTING; DNA SEQUENCE; GENE OVEREXPRESSION; GENETIC ALGORITHM; GENETIC REGULATION; HUMAN; MOLECULAR BIOLOGY; MOLECULAR PHYLOGENY; NONHUMAN; ORTHOLOGY; PROMOTER REGION; PROTEIN MOTIF; REGULATORY MECHANISM; YEAST; ALGORITHM; BINDING SITE; CHEMISTRY; COMPARATIVE STUDY; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; REVIEW; SEQUENCE ALIGNMENT;

ALGORITHMS; BASE SEQUENCE; BINDING SITES; DNA; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS;

EID: 38549144819     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-S7-S21     Document Type: Conference Paper

References (92)

1. Rombauts S Dehais P Van Montagu M Rouze P PlantCARE, a plant cis acting regulatory element database Nucleic Acids Res 1999 27 295-296 148162 9847207
2. Tagle D Koop B Goodman M Slightom J Hess D Jones R Embryonic ε and γ globin genes of a prosimian primate (Galago crassicaudatus): nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints J Mol Biol 1988 203 439-455 3199442
3. Cliften PF Hillier LW Fulton L Graves T Miner T Gish WR Waterston RH Johnston M Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis Genome Res 2001 11 1175-1186 11435399
4. Blanchette M Tompa M Discovery of regulatory elements by a computational method for phylogenetic footprinting Genome Res 2002 12 739-748 186562 11997340
5. Berezikov E Guryev V Plasterk RHA Cuppen E CONREAL: Conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting Genome Res 2004 14 170-178 314294 14672977
6. Cliften P Sudarsanam P Desikan A Fulton L Fulton B Majors J Waterston R Cohen BA Johnston M Finding functional features in Saccharomyces genomes by phylogenetic footprinting Science 2003 301 71-76 12775844
7. Wang T Stormo GD Identifying the conserved network of cis-regulatory sites of a eukaryotic genome PNAS 2005 102 17400-17405 1297658 16301543
8. Carmack CS McCue LA Newberg LA Lawrence CE PhyloScan: Identification of transcription factor binding sites using cross-species evidence Algorithms for Molecular Biology 2007 2 1 1794230 17244358
9. Gelfand MS Koonin EV Mironov AA Prediction of transcription regulatory sites in Archaea by a comparative genome approach Nucleic Acids Res 2000 28 695-705 102549 10637320
10. McGuire AM Hughes JD Church GM Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes Genome Res 2000 10 744-757 10854408
11. Kellis M Patterson N Endrizzi M Birren B Lander E Sequencing and comparison of yeast species to identify genes and regulatory element Nature 2003 423 241-254 12748633
12. Prakash A Blanchette M Sinha S Tompa M Motif discovery in heterogeneous sequence data Proceedings of the Ninth Pacific Symposium on Biocomputing 2004 348-359
13. Wang T Stormo GD Combining phylogenetic data with coregulated genes to identify regulatory motifs Bioinformatics 2003 19 2369-2380 14668220
14. Sinha S Blanchette M Tompa M PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences BMC Bioinformatics 2004 5 170 534098 15511292
15. Moses A Chiang D Eisen M Phylogenetic motif detection by expectation-maximization on evolutionary mixtures Proceedings of the Ninth Pacific Symposium on Biocomputing 2004 324-335
16. Siddharthan R Siggia ED van Nimwegen E PhyloGibbs: A Gibbs sampling motif finder that incorporates phylogeny PLoS Comput Biol 2005 1 534-556
17. Hon LS Jain AN A deterministic motif finding algorithm with application to the human genome Bioinformatics 2006 22 1047-1054 16455748
18. Stormo GD DNA binding sites: Representation and discovery Bioinformatics 2000 16 16-23 10812473
19. Sagot M Spelling approximate repeated or common motifs using a suffix tree Lecture Notes in Computer Science 1998 1380 111-127
20. Vilo J Brazma A Jonassen I Robinson A Ukonnen E Mining for putative regulatory elements in the yeast genome using gene expression data Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology AAAI Press San Diego, CA 2000 384-394
21. Bucher P Weight matrix description for four eukaryotic RNA polymerase II promoter element derived from 502 unrelated promoter sequences J Mol Biol 1990 212 563-578 2329577
22. Schneider TD Stephens RM Sequence logos: A new way to display consensus sequence Nucleic Acids Res 1990 18 6097-6100 332411 2172928
23. van Helden J Andre B Collado-Vides J Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies J Mol Biol 1998 281 827-842 9719638
24. van Helden J Rios AF Collado-Vides J Discovering regulatory elements in non-coding sequences by analysis of spaced dyads Nucleic Acids Res 2000 28 1808-1818 102821 10734201
25. Tompa M An exact method for finding short motifs in sequences, with application to the ribosome binding site problem Proceedings of the Seventh International Conference on Intelligent Systems on Molecular Biology 1999 262-271
26. Sinha S Tompa M A statistical method for finding transcription factor binding site Proceedings of the Eighth International Conference on Intelligent Systems on Molecular Biology, San Diego, CA 2000 344-354
27. Mewes HW Frishman D Guldener U Mannhaupt G Mayer K Mokrejs M Morgenstern B Munsterkotter M Rudd S Weil B MIPS: A database for genomes and protein sequences Nucleic Acids Res 2002 30 31-34 99165 11752246
28. Sinha S Tompa M Performance comparison of algorithms for finding transcription factor binding sites Third IEEE Symposium on Bioinformatics and Bioengineering IEEE Press 2003 214-220
29. Bailey TL Elkan C Unsupervised learning of multiple motifs in biopolymers using expectation maximization Machine Learning 1995 21 51-80
30. 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 16 939-945 9788350
31. Brazma A Jonassen I Vilo J Ukkonen E Predicting gene regulatory elements in silico on a genomic scale Genome Res 1998 8 1202-1215 310790 9847082
32. Vanet A Marsan L Labigne A Sagot MF Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori σ80 family of promoter signals J Mol Biol 2000 297 335-353 10715205
33. Marsan L Sagot M 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
34. Pavesi G Mauri G Pesole G An algorithm for finding signals of unknown length in DNA sequences Bioinformatics 2001 17 Suppl 1 S207-S214 11473011
35. Eskin E Pevzner P Finding composite regulatory patterns in DNA sequences Bioinformatics 2002 18 Suppl 1 S354-S363 12169566
36. Pevzner P Sze S Combinatorial approaches to finding subtle signals in DNA sequences Proceedings of the Eighth International Conference on Intelligent Systems on Molecular Biology, San Diego, CA 2000 269-278
37. Liang S cWINNOWER algorithm for finding fuzzy DNA motifs IEEE Computer Society Bioinformatics Conference 2003 260-265
38. Hertz GZ Hartzell GW Stormo GD Identification of consensus patterns in unaligned DNA sequences known to be functionally related Comput Appl Biosci 1990 6 81-92 2193692
39. Hertz GZ Stormo GD Identifying DNA and protein patterns with statistically significant alignments of multiple sequences Bioinformatics 1999 15 563-577 10487864
40. Down TA Hubbard TJP NestedMICA: Sensitive inference of over-represented motifs in nucleic acid sequence Nucleic Acids Res 2005 33 1445-1453 1064142 15760844
41. Lawrence CE Reilly AA An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences Proteins 1990 7 41-51 2184437
42. 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 262 208-214 8211139
43. Liu JS Monte Carlo Strategies in Scientific Computing Springer Series in Statistics 2001
44. Liu JS Neuwald AF Lawrence CE Bayesian models for multiple local sequence alignment and Gibbs sampling strategies J Amer Statist Assoc 1995 90 1156-1170
45. Hughes JD Estep PW Tavazoie S Church GM Computational identification of cis-regulatory elements associated with functionally coherent groups of genes in Saccharomyces cerevisiae J Mol Biol 2000 296 1205-1214 10698627
46. Thijs G Marchal K Moreau Y A Gibbs sampling method to detect over-represented motifs in upstream regions of co-expressed genes RECOMB 2001 5 305-312
47. Liu X Brutlag DL Liu JS BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes Proceedings of the Sixth Pacific Symposium on Biocomputing 2001 127-138
48. Shida K GibbsST: A Gibbs sampling method for motif discovery with enhanced resistance to local optima BMC Bioinformatics 2006 7 486 1647290 17083740
49. Buhler J Tompa M Finding motifs using random projections J Comput Biol 2002 9 225-242 12015879
50. Kirkpatrick S Gelatt CD Vecchi MP Optimization by simulated annealing Science 1983 220 671-680 17813860
51. Ishikawa M Toya T Hoshida M Nitta K Ogiwara A Kanehisa M Multiple sequence alignment by parallel simulated annealing Comput Appl Biosci 1993 9 267-273 8324627
52. Kim J Pramanik S Chung MJ Multiple sequence alignment using simulated annealing Comput Appl Biosci 1994 10 419-426 7804875
53. Liu FFM Tsai JJP Chen RM Chen SN Shih SH FMGA: Finding motifs by genetic algorithm Fourth IEEE Symposium on Bioinformatics and Bioengineering 2004 459
54. Liu D Xiong X DasGupta B Zhang H Motif discoveries in unaligned molecular sequences using self-organizing neural network IEEE Transactions on Neural Networks 2006 17 919-928 16856655
55. Kingsford C Zaslavsky E Singh M A compact mathematical programming formulation for DNA motif finding Lecture Notes in Computer Science 2006 4009 233-245
56. Kaplan T Friedman N Margalit H Ab initio prediction of transcription factor targets using structural knowledge PLoS Comput Biol 2005 1 1 e1 1183507 16103898
57. Tompa M Li N Bailey T Church GM De Moor B Eskin E Favorov A Frith MC 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 23 137-144 15637633
58. Hu J Li B Kihara D Limitations and potentials of current motif discovery algorithms Nucleic Acids Res 2005 33 4899-4913 1199555 16284194
59. Hu J Yang YD Kihara D EMD: An ensemble algorithm for discovering regulatory motifs in DNA sequences BMC Bioinformatics 2006 7 342 1539026 16839417
60. Liu XS Brutlag DL Liu JS An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments Nat Biotechnol 2002 20 835-839 12101404
61. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice Nucleic Acids Res 1994 22 4673 308517 7984417
62. Tompa M Identifying functional elements by comparative DNA sequence analysis Genome Res 2001 11 1143-1144 11435394
63. 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 29 774-782 30389 11160901
64. Brudno M Do CB Cooper GM Kim MF Davydov E NISC Comparative Sequencing Program Green ED Sidow A Batzoglou S LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA Genome Res 2003 13 721-731 430158 12654723
65. Bray N Dubchak I Pachter L AVID: A global alignment program Genome Res 2003 13 97-102 430967 12529311
66. Karlin S Altschul SF Methods for assessing the statistical significance of sequence features by using general scoring schemes PNAS 1990 87 2264-2268 53667 2315319
67. Thompson W Rouchka E Lawrence C Gibbs Recursive Sampler: Finding transcription factor binding sites Nucleic Acids Res 2003 31 3580-3585 169014 12824370
68. Workman CT Stormo GD ANN-Spec: A method for discovering transcription factor binding sites with improved specificity Proceedings of the Fifth Pacific Symposium on Biocomputing 2000 467-478
69. Frith MC Hansen U Spouge JL Weng Z Finding functional sequence elements by multiple local alignment Nucleic Acids Res 2004 32 189-200 373279 14704356
70. Ao W Gaudet J Kent WJ Muttumu S Mango SE Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR Science 2004 305 1743-1746 15375261
71. Regnier M Denise A Rare events and conditional events on random strings Discrete Math Theor Comput Sci 2004 6 191-214
72. Favorov AV Gelfand MS Gerasimova AV Mironov AA Makeev VJ Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length and its validation on the ArcA binding sites Proceedings of Fourth International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia 2004
73. Wingender E Dietze P Karas H Knuppel R TRANSFAC: A Database on transcription factors and their DNA binding sites Nucleic Acids Res 1996 24 238-241 145586 8594589
74. Galas DJ Eggert M Waterman MS Rigorous pattern-recognition methods for DNA sequences: Analysis of promoter sequences from Escherichia coli J Mol Biol 1985 186 117-128 3908689
75. Mengeritsky G Smith TF Recognition of characteristic patterns in sets of functionally equivalent DNA sequences Comput Appl Biosci 1987 3 223-227 3330960
76. Staden R Methods for discovering novel motif in nucleic acid sequences Comput Appl Biosci 1989 5 293-298 2684350
77. Pesole G Prunella N Liuni S Attimonelli M Saccon C WORDUP: An efficient algorithm for discovering statistically significant patterns in DNA sequences Nucleic Acids Res 1992 20 2871-2875 336935 1614873
78. Liu JS The collapsed Gibbs sampler in Bayesian computations with applications to a gene regulation problem J Amer Statist Assoc 1994 89 958-966
79. Apostolico A Bock M Lonardi S Xu X Efficient detection of unusual words J Comput Biol 2000 7 71-94 10890389
80. Bussemaker H Li H Siggia E Regulatory element detection using a probabilistic segmentation model Proceedings of the Eighth International Conference on Intelligent Systems on Molecular Biology, San Diego, CA 2000 67-74
81. GuhaThakurta D Stormo GD Identifying target sites for cooperatively binding factors Bioinformatics 2001 17 608-621 11448879
82. Kielbasa SM Korbel JO Beule D Schuchhardt J Herzel H Combining frequency and positional information to predict transcription factor binding sites Bioinformatics 2001 17 1019-1026 11724730
83. Ganesh R Siegele DA Ioerger TR MOPAC: Motif finding by preprocessing and agglomerative clustering from microarrays Proceedings of the Eighth Pacific Symposium on Biocomputing 2003 41-52
84. Sinha S Discriminative motifs J Comput Biol 2003 10 599-615 12935347
85. Xing EP Wu W Jordan MI Karp RM Logos: A modular Bayesian model for de novo motif detection J Bioinform Comput Biol 2004 2 127-154 15272436
86. Fogel GB Weekes DG Varga G Dow ER Harlow HB Onyia JE Su C Discovery of sequence motifs related to coexpression of genes using evolutionary computation Nucleic Acids Res 2004 32 3826-3835 506801 15266008
87. Qi Y Ye P Bader JS Genetic interaction motif finding by expectation maximization - a novel statistical model for inferring gene modules from synthetic lethality BMC Bioinformatics 2005 6 288 1334220 16332255
88. Wang G Yu T Zhang W WordSpy: Identifying transcription factor binding motifs by building a dictionary and learning a grammar Nucleic Acids Res 2005 33 Web Server W412-W416 1160252 15980501
89. Mendes ND Casimiro AC Santos PM Sa-Correira I Oliveira AL Freitas AT MUSA: A parameter free algorithm for the identification of biologically significant motifs Bioinformatics 2006 22 2996-3002 17068086
90. Wei Z Jensen ST GAME: Detecting cis-regulatory elements using a genetic algorithm Bioinformatics 2006 22 1577-1584 16632495
91. Leung HCM Chin FYL Finding motifs from all sequences with and without binding sites Bioinformatics 2006 22 2217-2223 16870937
92. Peng CH Hsu JT Chung YS Lin YJ Chow WY Hsu DF Tang CY Identification of degenerate motifs using position restricted selection and hybrid ranking combination Nucleic Acids Res 2006 34 6379-6391 1702486 17130169