메뉴 건너뛰기




Volumn 9, Issue SUPPL. 9, 2008, Pages

MTAP: The motif tool assessment platform

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC SEQUENCE; MOTIF DETECTIONS; MOTIF DISCOVERY; PERFORMANCE CHARACTERISTICS; PROOF OF CONCEPT; REGULATORY MOTIFS; SPECIFIC PROBLEMS; UPSTREAM SEQUENCE;

EID: 49649108913     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-S9-S6     Document Type: Conference Paper
Times cited : (10)

References (35)
  • 1
    • 0022358896 scopus 로고
    • Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli
    • 10.1016/0022-2836(85)90262-1 3908689
    • 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(1):117-128. 10.1016/0022-2836(85)90262-1 3908689
    • (1985) J Mol Biol , vol.186 , Issue.1 , pp. 117-128
    • Galas, D.J.1    Eggert, M.2    Waterman, M.S.3
  • 2
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • 10.1126/science.8211139 8211139
    • 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. 10.1126/ science.8211139 8211139
    • (1993) Science , vol.262 , Issue.5131 , pp. 208-214
    • Lawrence, C.E.1    Altschul, S.F.2    Boguski, M.S.3    Liu, J.S.4    Neuwald, A.F.5    Wootton, J.C.6
  • 3
    • 0043123063 scopus 로고    scopus 로고
    • Gibbs Recursive Sampler: Finding transcription factor binding sites
    • 169014 12824370 10.1093/nar/gkg608
    • Thompson W Rouchka E Lawrence C Gibbs Recursive Sampler: Finding transcription factor binding sites Nucl Acids Res 2003, 31(13):3580-3585. 169014 12824370 10.1093/nar/gkg608
    • (2003) Nucl Acids Res , vol.31 , Issue.13 , pp. 3580-3585
    • Thompson, W.1    Rouchka, E.2    Lawrence, C.3
  • 4
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolyme rs
    • 7584402
    • Bailey TL Elkan C Fitting a mixture model by expectation maximization to discover motifs in biopolyme rs Proc Int Conf Intell Syst Mol Biol 1994, 2:28-36. 7584402
    • (1994) Proc Int Conf Intell Syst Mol Biol , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 5
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • 10.1093/bioinformatics/15.7.563 10487864
    • Hertz G Stormo G Identifying DNA and protein patterns with statistically significant alignments of multiple sequences Bioinformatics 1999, 15(7):563-577. 10.1093/bioinformatics/15.7.563 10487864
    • (1999) Bioinformatics , vol.15 , Issue.7 , pp. 563-577
    • Hertz, G.1    Stormo, G.2
  • 6
    • 0025372992 scopus 로고
    • Identification of consensus patterns in unaligned DNA sequences known to be functionally related
    • 2193692
    • 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. 2193692
    • (1990) Comput Appl Biosci , vol.6 , Issue.2 , pp. 81-92
    • Hertz, G.Z.1    Hartzell, G.W.2    Stormo, G.D.3
  • 7
    • 0035228215 scopus 로고    scopus 로고
    • BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    • 11262934
    • Liu X Brutlag DL Liu JS BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes Pac Symp Biocomput 2001, 127-138. 11262934
    • (2001) Pac Symp Biocomput , pp. 127-138
    • Liu, X.1    Brutlag, D.L.2    Liu, J.S.3
  • 8
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    • 10.1006/jmbi.2000.3519 10698627
    • Hughes JD Estep PW Tavazoie S Church GM Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae J Mol Biol 2000, 296(5):1205-1214. 10.1006/jmbi.2000.3519 10698627
    • (2000) J Mol Biol , vol.296 , Issue.5 , pp. 1205-1214
    • Hughes, J.D.1    Estep, P.W.2    Tavazoie, S.3    Church, G.M.4
  • 9
    • 0033655171 scopus 로고    scopus 로고
    • ANN-Spec: A method for discovering transcription factor binding sites with improved specificity
    • 10902194
    • Workman CT Stormo GD ANN-Spec: A method for discovering transcription factor binding sites with improved specificity Pac Symp Biocomput 2000, 467-478. 10902194
    • (2000) Pac Symp Biocomput , pp. 467-478
    • Workman, C.T.1    Stormo, G.D.2
  • 10
    • 1242264319 scopus 로고    scopus 로고
    • Finding functional sequence elements by multiple local alignme nt
    • 373279 14704356 10.1093/nar/gkh169
    • Frith MC Hansen U Spouge JL Weng Z Finding functional sequence elements by multiple local alignme nt Nucleic Acids Res 2004, 32(1):189-200. 373279 14704356 10.1093/nar/gkh169
    • (2004) Nucleic Acids Res , vol.32 , Issue.1 , pp. 189-200
    • Frith, M.C.1    Hansen, U.2    Spouge, J.L.3    Weng, Z.4
  • 11
    • 0035224579 scopus 로고    scopus 로고
    • An algorithm for finding signals of unknown length in DNA sequences
    • 11473011
    • Pavesi G Mauri G Pesole G An algorithm for finding signals of unknown length in DNA sequences Bioinformatics 2001, 17(Suppl 1). 11473011
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Pavesi, G.1    Mauri, G.2    Pesole, G.3
  • 12
    • 3242884167 scopus 로고    scopus 로고
    • Weeder Web: Discovery of transcription factor binding sites in a set of sequences from co-regulated genes
    • Web Server
    • 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. Web Server
    • (2004) Nucleic Acids Res , pp. 32
    • Pavesi, G.1    Mereghetti, P.2    Mauri, G.3    Pesole, G.4
  • 13
    • 20844455471 scopus 로고    scopus 로고
    • BEST: Binding-site Estimation Suite of Tools
    • 10.1093/bioinformatics/bti425 15814553
    • Che D Jensen S Cai L Liu J BEST: Binding-site Estimation Suite of Tools Bioinformatics 2005, 21(12):2909-2911. 10.1093/bioinformatics/bti425 15814553
    • (2005) Bioinformatics , vol.21 , Issue.12 , pp. 2909-2911
    • Che, D.1    Jensen, S.2    Cai, L.3    Liu, J.4
  • 14
    • 33847107996 scopus 로고    scopus 로고
    • EMD: An ensemble algorithm for discovering regulatory motifs in DNA sequences
    • 1539026 16839417 10.1186/1471-2105-7-342
    • Hu J Yang Y Kihara D EMD: An ensemble algorithm for discovering regulatory motifs in DNA sequences BMC Bioinformatics 2006, 7:342. 1539026 16839417 10.1186/1471-2105-7-342
    • (2006) BMC Bioinformatics , vol.7 , pp. 342
    • Hu, J.1    Yang, Y.2    Kihara, D.3
  • 15
    • 13244260826 scopus 로고    scopus 로고
    • PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
    • Sinha S Blanchette M Tompa M PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences BMC Bioinformatics 2004, 5.
    • (2004) BMC Bioinformatics , pp. 5
    • Sinha, S.1    Blanchette, M.2    Tompa, M.3
  • 16
    • 33750218960 scopus 로고    scopus 로고
    • PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
    • 1309704 16477324
    • Siddharthan R Siggia ED van Nimwegen E PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny PLoS Comput Biol 2005, 1:7. 1309704 16477324
    • (2005) PLoS Comput Biol , vol.1
    • Siddharthan, R.1    Siggia, E.D.2    van Nimwegen, E.3
  • 17
    • 33847664259 scopus 로고    scopus 로고
    • WeederH: An algorithm for finding conserved regulatory motifs and regions in homologous sequences
    • 1803799 17286865 10.1186/1471-2105-8-46
    • Pavesi G Zambelli F Pesole G WeederH: An algorithm for finding conserved regulatory motifs and regions in homologous sequences BMC Bioinformatics 2007, 8:46. 1803799 17286865 10.1186/1471-2105-8-46
    • (2007) BMC Bioinformatics , vol.8 , pp. 46
    • Pavesi, G.1    Zambelli, F.2    Pesole, G.3
  • 18
    • 0043123144 scopus 로고    scopus 로고
    • REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data
    • 169192 12824350 10.1093/nar/gkg630
    • Roven C Bussemaker HJ REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data Nucleic Acids Res 2003, 31(13):3487-3490. 169192 12824350 10.1093/nar/gkg630
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3487-3490
    • Roven, C.1    Bussemaker, H.J.2
  • 21
    • 34347339593 scopus 로고    scopus 로고
    • Improved benchmarks for computational motif discovery
    • 1903367 17559676 10.1186/1471-2105-8-193
    • Sandve G Abul O Walseng V Drablos F Improved benchmarks for computational motif discovery BMC Bioinformatics 2007, 8:193. 1903367 17559676 10.1186/1471-2105-8-193
    • (2007) BMC Bioinformatics , vol.8 , pp. 193
    • Sandve, G.1    Abul, O.2    Walseng, V.3    Drablos, F.4
  • 23
    • 26444584579 scopus 로고    scopus 로고
    • Limitations and potentials of current motif discovery algorithms
    • 1199555 16284194 10.1093/nar/gki791
    • Hu J Li B Kihara D Limitations and potentials of current motif discovery algorithms Nucleic Acids Research 2005, 33(15):4899-4913. 1199555 16284194 10.1093/nar/gki791
    • (2005) Nucleic Acids Research , vol.33 , Issue.15 , pp. 4899-4913
    • Hu, J.1    Li, B.2    Kihara, D.3
  • 25
    • 34848865681 scopus 로고    scopus 로고
    • Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes
    • 10.1371/journal.pcbi.0030175
    • Price M Dehal P Arkin A Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes PLoS Computational Biology 2007, 3(9):e175. 10.1371/journal.pcbi.0030175
    • (2007) PLoS Computational Biology , vol.3 , Issue.9
    • Price, M.1    Dehal, P.2    Arkin, A.3
  • 27
    • 0035170506 scopus 로고    scopus 로고
    • DBTBS: A database of Bacillus subtilis promoters and transcription factors
    • 29858 11125112 10.1093/nar/29.1.278
    • Ishii T Yoshida K-I Terai G Fujita Y Nakai K DBTBS: A database of Bacillus subtilis promoters and transcription factors Nucl Acids Res 2001, 29(1):278-280. 29858 11125112 10.1093/nar/29.1.278
    • (2001) Nucl Acids Res , vol.29 , Issue.1 , pp. 278-280
    • Ishii, T.1    Yoshida, K.-I.2    Terai, G.3    Fujita, Y.4    Nakai, K.5
  • 28
  • 30
    • 0029960055 scopus 로고    scopus 로고
    • TRANSFAC: A database on transcription factors and their DNA binding sites
    • 145586 8594589 10.1093/nar/24.1.238
    • Wingender E Dietze P Karas H Knuppel R TRANSFAC: A database on transcription factors and their DNA binding sites Nucleic Acids Res 1996, 24(1):238-241. 145586 8594589 10.1093/nar/24.1.238
    • (1996) Nucleic Acids Res , vol.24 , Issue.1 , pp. 238-241
    • Wingender, E.1    Dietze, P.2    Karas, H.3    Knuppel, R.4
  • 31
    • 0141626909 scopus 로고    scopus 로고
    • Detecting putative orthologs
    • 10.1093/bioinformatics/btg213 15593400
    • Wall DP Fraser HB Hirsh AE Detecting putative orthologs Bioinformatics 2003, 19(13):1710-1711. 10.1093/bioinformatics/btg213 15593400
    • (2003) Bioinformatics , vol.19 , Issue.13 , pp. 1710-1711
    • Wall, D.P.1    Fraser, H.B.2    Hirsh, A.E.3
  • 33
    • 33747823564 scopus 로고    scopus 로고
    • MEME: Discovering and analyzing DNA and protein sequence motifs
    • (Web Server issue) 1538909 16845028 10.1093/nar/gkl198
    • Bailey TL Williams N Misleh C Li WW MEME: Discovering and analyzing DNA and protein sequence motifs Nucleic Acids Res 2006, 34(Web Server issue):W369-W373. 1538909 16845028 10.1093/nar/gkl198
    • (2006) Nucleic Acids Res , vol.34
    • Bailey, T.L.1    Williams, N.2    Misleh, C.3    Li, W.W.4
  • 34
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • 10.1016/j.patrec.2005.10.010
    • Fawcett T An introduction to ROC analysis ROC Analysis in Pattern Recognition 2006, 27(8):861-874. 10.1016/j.patrec.2005.10.010
    • (2006) ROC Analysis in Pattern Recognition , vol.27 , Issue.8 , pp. 861-874
    • Fawcett, T.1
  • 35
    • 3242687409 scopus 로고    scopus 로고
    • Logos: A modular bayesian model for de novo motif detection
    • 10.1142/S0219720004000508 15272436
    • Xing EP Wu W Jordan MI Karp RM Logos: A modular bayesian model for de novo motif detection J Bioinform Comput Biol 2004, 2(1):127-154. 10.1142/ S0219720004000508 15272436
    • (2004) J Bioinform Comput Biol , vol.2 , Issue.1 , pp. 127-154
    • Xing, E.P.1    Wu, W.2    Jordan, M.I.3    Karp, R.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.