ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes

作者: I. Ovcharenko , M. A. Nobrega , G. G. Loots , L. Stubbs

DOI: 10.1093/NAR/GKH355

关键词: Computational biologyAnnotationGeneGenomeBiologyVertebrate and Genome Annotation ProjectSequence alignmentDNA binding siteGeneticsDNA sequencingSequence analysis

摘要: … ECRs, we have introduced the ‘Grab ECR’ option, which allows ‘one-click’ access to any selected ECR … This option connects to a detailed ECR description page containing ECR …

参考文章(30)
Scott Schwartz, Zheng Zhang, Kelly A Frazer, Arian Smit, Cathy Riemer, John Bouck, Richard Gibbs, Ross Hardison, Webb Miller, PipMaker—A Web Server for Aligning Two Genomic DNA Sequences Genome Research. ,vol. 10, pp. 577- 586 ,(2000) , 10.1101/GR.10.4.577
J. W. Thomas, J. W. Touchman, R. W. Blakesley, G. G. Bouffard, S. M. Beckstrom-Sternberg, E. H. Margulies, M. Blanchette, A. C. Siepel, P. J. Thomas, J. C. McDowell, B. Maskeri, N. F. Hansen, M. S. Schwartz, R. J. Weber, W. J. Kent, D. Karolchik, T. C. Bruen, R. Bevan, D. J. Cutler, S. Schwartz, L. Elnitski, J. R. Idol, A. B. Prasad, S.-Q. Lee-Lin, V. V. B. Maduro, T. J. Summers, M. E. Portnoy, N. L. Dietrich, N. Akhter, K. Ayele, B. Benjamin, K. Cariaga, C. P. Brinkley, S. Y. Brooks, S. Granite, X. Guan, J. Gupta, P. Haghighi, S.-L. Ho, M. C. Huang, E. Karlins, P. L. Laric, R. Legaspi, M. J. Lim, Q. L. Maduro, C. A. Masiello, S. D. Mastrian, J. C. McCloskey, R. Pearson, S. Stantripop, E. E. Tiongson, J. T. Tran, C. Tsurgeon, J. L. Vogt, M. A. Walker, K. D. Wetherby, L. S. Wiggins, A. C. Young, L.-H. Zhang, K. Osoegawa, B. Zhu, B. Zhao, C. L. Shu, P. J. De Jong, C. E. Lawrence, A. F. Smit, A. Chakravarti, D. Haussler, P. Green, W. Miller, E. D. Green, Comparative analyses of multi-species sequences from targeted genomic regions Nature. ,vol. 424, pp. 788- 793 ,(2003) , 10.1038/NATURE01858
Laura Elnitski, Jin Li, Constance Tom Noguchi, Webb Miller, Ross Hardison, A Negative Cis-element Regulates the Level of Enhancement by Hypersensitive Site 2 of the β-Globin Locus Control Region Journal of Biological Chemistry. ,vol. 276, pp. 6289- 6298 ,(2001) , 10.1074/JBC.M009624200
Edgar Wingender, Peter Dietze, Holger Karas, Rainer Knüppel, TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Research. ,vol. 24, pp. 238- 241 ,(1996) , 10.1093/NAR/24.1.238
Olivier Couronne, Alexander Poliakov, Nicolas Bray, Tigran Ishkhanov, Dmitriy Ryaboy, Edward Rubin, Lior Pachter, Inna Dubchak, Strategies and Tools for Whole-Genome Alignments Genome Research. ,vol. 13, pp. 73- 80 ,(2003) , 10.1101/GR.762503
Gabriela G Loots, Richard M Locksley, Cathy M Blankespoor, Zhi-En Wang, Webb Miller, Edward M Rubin, Kelly A Frazer, Identification of a Coordinate Regulator of Interleukins 4, 13, and 5 by Cross-Species Sequence Comparisons Science. ,vol. 288, pp. 136- 140 ,(2000) , 10.1126/SCIENCE.288.5463.136
Noël Ghanem, Olga Jarinova, Angel Amores, Qiaoming Long, Gary Hatch, Byung Keon Park, John LR Rubenstein, Marc Ekker, Regulatory Roles of Conserved Intergenic Domains in Vertebrate Dlx Bigene Clusters Genome Research. ,vol. 13, pp. 533- 543 ,(2003) , 10.1101/GR.716103
Len A Pennacchio, Michael Olivier, Jaroslav A Hubacek, Jonathan C Cohen, David R Cox, Jean-Charles Fruchart, Ronald M Krauss, Edward M Rubin, An Apolipoprotein Influencing Triglycerides in Humans and Mice Revealed by Comparative Sequencing Science. ,vol. 294, pp. 169- 173 ,(2001) , 10.1126/SCIENCE.1064852
Laura Elnitski, Ross C Hardison, Jia Li, Shan Yang, Diana Kolbe, Pallavi Eswara, Michael J O'Connor, Scott Schwartz, Webb Miller, Francesca Chiaromonte, Distinguishing Regulatory DNA From Neutral Sites Genome Research. ,vol. 13, pp. 64- 72 ,(2003) , 10.1101/GR.817703
S Altschula, Warren Gisha, Webb Millerb, E Meyersc, D Lipmana, None, Basic Local Alignment Search Tool Journal of Molecular Biology. ,vol. 215, pp. 403- 410 ,(1990) , 10.1016/S0022-2836(05)80360-2