COTRASIF

TFBS finder

Version history:

v0.22 (Dec 5, 2009)
v0.21 (Oct 11, 2009)
v0.20 (May 23, 2009)
v0.18 (Mar 08, 2009)
v0.17 (Jan 19, 2009)
v0.16 (Oct 31, 2008)
v0.14 (Apr 14, 2008)
v0.13 (Mar 31, 2008)
v0.12 (Jan 28, 2008)
v0.11 (Nov 22, 2007)
v0.10 (Sep 18, 2007)

References

• Gang Su, Binchen Mao, and Jin Wang. A web server for transcription factor binding site prediction // Bioinformation.-2006.-1, 5.-P. 156-157.
• Zhao, F., Xuan, Z., Liu, L., and Zhang, M. Q. TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies // Nucleic Acids Research.-2005.-33, suppl_1.-P. D103-D107.
• Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W. W., and Lenhard, B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles // Nucleic Acids Research.-2004.-32, suppl_1.-P. D91-D94.
• Lenhard, B. and Wasserman, W. W. TFBS: Computational framework for transcription factor binding site analysis // Bioinformatics.-2002.-18, 8.-P. 1135-1136.
• Schones, D. E., Sumazin, P., and Zhang, M. Q. Similarity of position frequency matrices for transcription factor binding sites // Bioinformatics.-2005.-21, 3.-P. 307-313.
• Stormo, G. D. DNA binding sites: representation and discovery // Bioinformatics.-2000.-16, 1.-P. 16-23.
• Staden, R. Computer methods to locate signals in nucleic acid sequences // Nucleic Acids Research.-1984.-12, 1Part2.-P. 505-519.
• Stormo, G. D., Schneider, T. D., Gold, L., and Ehrenfeucht, A. Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli // Nucleic Acids Research.-1982.-10, 9.-P. 2997-3011.
• Hertz, G. Z. and Stormo, G. D. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences // Bioinformatics.-1999.-15, 7.-P. 563-577.
• Hertz, G. Z., Hartzell, G. W., III, and Stormo, G. D. Identification of consensus patterns in unaligned DNA sequences known to be functionally related // Bioinformatics.-1990.-6, 2.-P. 81-92.
• Stormo, G. D. and Hartzell, G. W. Identifying Protein-Binding Sites from Unaligned DNA Fragments // Proceedings of the National Academy of Sciences.-1989.-86, 4.-P. 1183-1187.
• Matys, V., Kel-Margoulis, O. V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K., Voss, N., Stegmaier, P., Lewicki-Potapov, B., Saxel, H., Kel, A. E., and Wingender, E. TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes // Nucleic Acids Research.-2006.-34, suppl_1.-P. D108-D110.
• Liu, X. S., Brutlag, D. L., and Liu, J. S. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments // Nat Biotech.-2002.-20, 8.-P. 835-839.
• J.van Helden, B.Andre, and J.Collado-Vides. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies // J Mol Biol.-2006.-281, 5.-P. 827-842.
• Pilpel, Y., Sudarsanam, P., and Church, G. M. Identifying regulatory networks by combinatorial analysis of promoter elements // Nat Genet.-2001.-29, 2.-P. 153-159.
• Bussemaker, H. J., Li, H., and Siggia, E. D. Regulatory element detection using correlation with expression // Nat Genet.-2001.-27, 2.-P. 167-174.
• Furman, I. and Pilpel, Y. Promoting human promoters // Mol Syst Biol.-2006.-2,P. E1-E2.
• Zhang, M. Q. Computational prediction of eukaryotic protein-coding genes // Nature Reviews Genetics.-2002.-3, 9.-P. 698-709.
• Cartharius, K., Frech, K., Grote, K., Klocke, B., Haltmeier, M., Klingenhoff, A., Frisch, M., Bayerlein, M., and Werner, T. MatInspector and beyond: promoter analysis based on transcription factor binding sites // Bioinformatics.-2005.-21, 13.-P. 2933-2942.
• Kel, A. E., Gossling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O. V., and Wingender, E. MATCHTM: a tool for searching transcription factor binding sites in DNA sequences // Nucleic Acids Research.-2003.-31, 13.-P. 3576-3579.
• Sandelin, A., Wasserman, W. W., and Lenhard, B. ConSite: web-based prediction of regulatory elements using cross-species comparison // Nucleic Acids Research.-2004.-32, suppl_2.-P. W249-W252.
• Curwen, V., Eyras, E., Andrews, T. D., Clarke, L., Mongin, E., Searle, S. M. J., and Clamp, M. The Ensembl Automatic Gene Annotation System // Genome Research.-2004.-14, 5.-P. 942-950.
• Jin, V. X., Leu, Y. W., Liyanarachchi, S., Sun, H., Fan, M., Nephew, K. P., Huang, T. H. M., and Davuluri, R. V. Identifying estrogen receptor {alpha} target genes using integrated computational genomics and chromatin immunoprecipitation microarray // Nucleic Acids Research.-2004.-32, 22.-P. 6627-6635.

© 2007 - 2010
Bogdan Tokovenko, Rostyslav Golda, Protas Oleksiy.