- Volume 9 Issue 5
Located on the upstream of a gene, the promoter region that plays a very important role in the control of gene expression as a signal part has various binding sites for transcription factors. These binding sites are present in various parts of the promoter region and assume an aspect of highly conserved consensus sequence pattern. This paper deals with the introductions of search methods for consensus pattern, including Wataru method, EM algorithm, MEME algorithm, Genetic algorithm and Phylogenetic Footprinting method, and intends to give future prospects of research on this field.
- G. Yi, S. H. Sze and M. R. Thon, "Identifying Clusters of Functionally Related Genes in Genomes", Bioinformatics 23(9), pp. 1053-1060, 2007. https://doi.org/10.1093/bioinformatics/btl673
- Michael Q. Zhan, "Computational Analyses of Eukaryotic Promoters", BMC Bioinformatics, 8:S3, 2007.
- D. Ghosh, "Object-oriented Transcription Factors Dabase(ooTFD)", Nucleic Acids Res. 28(1), pp. 308-310, 2000. https://doi.org/10.1093/nar/28.1.308
- V. Matys, et al., "TRNASFAC: Transcriptional Regulation, from Patterns to Profiles", Nucleic Acids Res. 31(1), pp. 374-378, 2003. https://doi.org/10.1093/nar/gkg108
- S. Gama-Castro, et al., "RegulonDB(version 6.0): Gene Regulation Model of Escherichia coli K-12 beyond Transcription, Active(Experimental) Annotated Promoters and Textpresso Navigation", Nucleic Acids Res., D:120-124, 2008.
- Fujibuchi Wataru and Minoru Kanehisa, "Prediction of Gene Expression Specificity by Promoter Sequence Patterns", DNA Research 4, pp. 81-90, 1997. https://doi.org/10.1093/dnares/4.2.81
- P. Horton and F. Wataru, “An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery”, CPM, pp.219-228, 2005.
- Lon R. Cardon and Gary D. Stormo, "Expectation Maximization Algorithm for Identifying Protein-binding Sites with Variable Lengths from Unaligned DNA Fragments", Journal of Molecular Biology, Vol. 223, pp. 159-170, 1992. https://doi.org/10.1016/0022-2836(92)90723-W
- Timothy Bailey and Charles Elkan, "Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization", Machine learning Journal, Vol. 21, pp. 51-83, 1995.
- T. Bailey, N. Williams, C. Misleh, and W. Li, “MEME: Discovering and Analyzing DNA and Protein Sequence Motifs”, Nucleic Acids Research, 34:W369-W373, 2006. https://doi.org/10.1093/nar/gkl198
- Jiang Liu, “A Combinatorial Approach for Motif Discovery in Unaligned DNA Sequences”, Thesis for the degree of master of mathematics, Univ. of Waterloo, Canada, 2004.
- David Beasley, David R. Bull and Ralph R. Martin, “An Overview of Genetic Algorithms”, University Computing, Vol. 15, No. 2, pp. 58-69, 1993.
- 김기봉, 공은배, “유전자 알고리즘을 이용한 프로모터 영역의 전사인자 결합부위 패턴 탐색”, 정보과학회논문지( 소프트웨어 및 응용 ), 제30권, 제5.6호, pp. 487-496, 2003
- M. R. Berthold, H. J. Lenz, E. Bradley, R. Kruse and C. Borgelt, “Advances in Intelligent Data Analysis V”, Springer Press, 2003.
- Wyeth W. Wasserman and ALbin Sandelin, “Applied Bioinformatics for the Identification of Regulatory Elements”, Nature Review Genetics, pp. 276-287, 2004. https://doi.org/10.1038/nrg1315
- Boris Lenhard, Albin Sandelin, Luis Mendoza, Par Engstrom, Niclas Jareborg and Wyeth W. Wasserman, “Identification of Conserved Regulatory Elements by Comparative Genome Analysis”, Journal of Biology, Vol. 2, pp. 13, 2003. https://doi.org/10.1186/1475-4924-2-13
- Alona Sosinsky, Barry Honing, Richard S. Mann and Andrea Califano, “Discovering Transcriptional Regulatory Regions in Drosophila by a Nonalignment Method for Phylogenetic Footprinting”, Proc. Natl. Acad. Sci. U.S.A., 104(15), pp. 6305-6310, 2007. https://doi.org/10.1073/pnas.0701614104
- Extended hybrid genetic algorithm for solving Travelling Salesman Problem with sorted population vol.11, pp.6, 2010, https://doi.org/10.5762/KAIS.2010.11.6.2269