95
Views
3
CrossRef citations to date
0
Altmetric
Original

BSS-HMM3s: An improved HMM method for identifying transcription factor binding sites

Full Length Research paper

, , , , &
Pages 403-411 | Received 09 Jun 2005, Published online: 11 Jul 2009

References

  • Baldi P, Brunak S. Bioinformatics: The Machine Learning Approach. The MIT Press, USA 2001; 145–195
  • George C, Roger LB. Statistical Inference2nd ed. Thomson Learning, Boston 2002; 109–200
  • Huang H, Tudor M, Weiss CA, et al. The Arabidopsis MADS-box gene AGL3 is widely expressed and encodes a sequence-specific DNA-binding protein. Plant Mol Biol 1995; 28: 549–567
  • Ikeda K, Kawakami K. DNA binding through distinct domains of zinc-finger-homeodomain protein AREB6 has different effects on gene transcription. Eur J Biochem 1995; 233: 73–82
  • Lu Q, Wright DD, Kamps MP. Fusion with E2A converts the Pbx1 homeodomain protein into a constitutive transcriptional activator in human leukemias carrying the t(1;19) translocation. Mol Cell Biol 1994; 14: 3938–3948
  • Mauhin V, Lutz Y, Dennefeld C, et al. Definition of the DNA-binding site repertoire for the Drosophila transcription factor SNAIL. Nucleic Acids Res 1993; 21: 3951–3957
  • Mertin S, McDowall SG, Harley VR. The DNA-binding specificity of SOX9 and other SOX proteins. Nucleic Acids Res 1999; 27: 1359–1364
  • Perez-Sanchez C, Gomez-Ferreria MA, de La Fuente CA, et al. FHX, a novel fork head factor with a dual DNA binding specificity. J Biol Chem 2000; 275: 12909–12916
  • Peterson RS, Lim L, Ye H, et al. The winged helix transcriptional activator HFH-8 is expressed in the mesoderm of the primitive streak stage of mouse embryos and its cellular derivatives. Mech Dev 1997; 69: 53–69
  • Quandt K, Frech K, Karas H, et al. MatInd and MatInspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res 1995; 23: 4878–4884
  • Rogozin IB, D'Angelo D, Milanesi L. Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences. Gene 1999; 226: 129–137
  • Rooney RJ, Raychaudhuri P, Nevins JR. E4F and ATF, two transcription factors that recognize the same site, can be distinguished both physically and functionally: A role for E4F in E1A trans activation. Mol Cell Biol 1990; 10: 5138–5149
  • Santoro IM, Yi TM, Walsh K. Identification of single-stranded-DNA-binding proteins that interact with muscle gene elements. Mol Cell Biol 1991; 11: 1944–1953
  • Sean RE. Profile hidden Markov models. Bioinformatics 1998; 14: 755–763
  • Shinozaki D, Akutsu T, Maruyama O. Finding optimal degenerate patterns in DNA sequences. Bioinformatics 2003; 19: ii206–ii214
  • Sinha S, Tompa M. A statistical method for finding transcription factor binding sites. Proc Int Conf Intell Syst Mol Biol 2000; 8: 344–354
  • Sinha S, van Nimwegen E, Siggia ED. A probabilistic method to detect regulatory modules. Bioinformatics 2003; 19: i292–i301
  • Solomon DL, Amati B, Land H. Distinct DNA binding preferences for the c-Myc/Max and Max/Max dimmers. Nucleic Acids Res 1993; 21: 5372–5376
  • Stormo GD. DNA binding sites: Representation and discovery. Bioinformatics 2000; 16: 16–23
  • Thakurta DG, Stormo GD. Identifying target sites for cooperatively binding factors. Bioinformatics 2001; 17: 608–621
  • Wagner A. Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics 1999; 15: 776–784
  • Yada T, Nakao M, Totoki Y, et al. Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models. Bioinformatics 1999; 15: 987–993

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.