Abstract
Sequence algorithms are widely used to study genomic sequences in such fields as DNA fragment assembly, genomic sequence similarities, motif search, etc. In this paper, we propose an algorithm that predicts transcription factor binding sites from a given set of sequences of upstream regions of genes using sequence algorithms, suffix arrays and the Smith-Waterman algorithm.
This work was supported by INHA UNIVERSITY Research Grant (INHA-32744).
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Batzoglou, S., Jaffe, D., Stanley, K., Butler, J., Gnerre, S., Mauceli, E., Berger, B., Mesirov, J., Lander, E.: Arachne: Awhole-genome shotgun assembler. Genome Research 12, 177–189 (2002)
Chen, T., Skiena, S.S.: Trie-based data structures for sequence assembly. In: Hein, J., Apostolico, A. (eds.) CPM 1997. LNCS, vol. 1264, pp. 206–223. Springer, Heidelberg (1997)
Green, P.: Documentation for phrap, Genome Center, University of Washington, http://www.phrap.org/phrap.docs/phrap.html
Gusfield, D.: Algorithms on Strings, Trees, and Sequences. Cambridge University Press, Cambridge (1997)
Ko, P., Aluru, S.: Space Efficient Linear Time Construction of Suffix Arrays. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 200–210. Springer, Heidelberg (2003)
Kato, M., Hata, N., Banerjee, N., Futcher, B., Zhang, M.Q.: Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biology 5(8), R56 (2004)
Kärkkäinen, J., Sanders, P.: Simple linear work suffix array construction, In: International Colloquium on Automata, Languages and Programming, LNCS, vol. 2676, pp. 943–955 (2003)
Kim, D.K., Sim, J.S., Park, H., Park, K.: Constructing suffix arrays in linear time. Journal of Discrete Algorithms 3, 126–142 (2005)
Lipman, D., Pearson, W.: Improved tools for biological sequence comparison. Proc. National Academy of Science 85, 2444–2448 (1988)
Manber, U., Myers, G.: Suffix arrays: A new method for on-line string searches. SIAM Journal on Computing 22, 935–938 (1993)
Matys, V., Fricke, E., Geffers, R., Goling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A.E., Kel-Margoulis, O.V., Kloos, D.U., Land, S., Lewicki-Potapov, B., Michael, H., Munch, R., Reuter, I., Rotert, S., Saxel, H., Scheer, M., Thiele, S., Wingender, E.: TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Research 31(1), 374–378 (2003)
Ohler, U., Niemann, H., Liao, G., Rubin, G.M.: Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics 17 (Suppl. 1), 199–206 (2001)
Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. Journal of Molecular Biology 147, 195–197 (1981)
Stoesser, G., Baker, W., Broek, A., Garcia-Pastor, M., Kanz, C., Kulikova, T., Leinonen, R., Lin, Q., Lombard, V., Lopez, R., Mancuso, R., Nardone, F., Stoehr, P., Tuli, M.A., Tzouvara, K., Vaughan, R.: The EMBL ncleotide sequence database: major new developments. Nucleic Acids Research 31(1), 17–22 (2003)
Zhang, M.Q.: Identification of human gene core promoters in silico. Genome Research 8(3), 319–326 (1998)
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Sim, J.S., Park, SJ. (2006). Transcription Factor Binding Sites Prediction Based on Sequence Similarity. In: Wang, L., Jiao, L., Shi, G., Li, X., Liu, J. (eds) Fuzzy Systems and Knowledge Discovery. FSKD 2006. Lecture Notes in Computer Science(), vol 4223. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11881599_131
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DOI: https://doi.org/10.1007/11881599_131
Publisher Name: Springer, Berlin, Heidelberg
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