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http://dx.doi.org/10.14400/JDC.2014.12.12.265

An Efficient Suffix Tree Reconstructing Algorithm for Biological Sequence Analysis  

Choi, Hae-Won (Dept. of Computer Engineering Kyungwoon University)
Jung, Young-Seok (Dept. of Computer Engineering Kyungwoon University)
Kim, Sang-Jin (Dept. of Computer Engineering Kyungwoon University)
Publication Information
Journal of Digital Convergence / v.12, no.12, 2014 , pp. 265-275 More about this Journal
Abstract
This paper introduces a new algorithms for reconstructing the suffix tree of character string, when a substring id deleted from the string or a string is inserted into the string as a substring. The algorithem has two main functions, delete-structure and insert-structure. The main objective of this algorithm is to save the time for constructing the suffix tree of an edited string, when the suffix tree of the original string is available. We tested the performance of this algorithm with some DNA sequences. This test shows that delete-reconstructing can save time when the length of the subsequence deleted is less than 30% of the original sequence, and the insert-reconstructing takes less time with regard to the length of inserted sequence.
Keywords
Suffix Tree; Ukkonen Algorithm; DNA Sequence; Biological Sequence;
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Times Cited By KSCI : 2  (Citation Analysis)
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1 D. Gusfield, Algorithm on String, Tree, and Sequence, Cambridge University Press, pp. 87-107, 1997.
2 David W., Bioinformatics, sequences and Genome Analysis, MOUNT Press, 2001.
3 Younshin Oh, Dinh Truong Nguyen, Identification of 1,531 cSNPs from Full-length Enriched cDNA Libraries of the Korean Native Pig Using in Silico Analysis, Genomics & Informatics, vol. 7, no. 2, 2009, pp. 65-84.   DOI   ScienceOn
4 Josue Samayoa, Fitnat H. Yildiz and Kevin Karplus, Identification of prokaryotic small proteins using a comparative genomic approach, Bioinformatics, vol.27, no.13, 2011, pp. 1765-1771.   DOI   ScienceOn
5 Chan Park, Ji-Seong Jeong, Design and Implementation of Bio-Medical Data Measurement System through the Stereo Microscope, Korea Contents Association KISTI-KOCON ICCC2009, November, vol.7, no.2, 2009, pp. 357-360.
6 Young-Ohk Song, Sung-young Kim and Duk-Jin Chang, Design of the System and Algorithm for the Pattern Analysis of the Bio-Data, Korea Contents Association, November, vol.10, no.8, 2008, pp. 104-110.   과학기술학회마을   DOI   ScienceOn
7 Audry P. G., Alan M.M., Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi, PLOS Biology, vol. 2, no. 12, 2004, pp. 398-405.   DOI   ScienceOn
8 Ketil Malde, Eivind Coward and Inge Jonassen, Fast sequence clustring using suffix array algorithm, Bioinformatics, 2003, pp. 1221-1226.
9 E. Ukkonen. On-line construction of suffix-trees. Algorithmica, 1995, pp. 249-67.
10 E.M. McCreight, A Space-Economical Suffix Tree Construction Algorithm. Journal of the ACM, vol. 23, no.2, 1976, pp. 262-272.   DOI   ScienceOn
11 R.A.Gibbs and S.Kurtz, From Ukkonen to McCreight and Weiner: A unifying view of linear-time suffix tree construction, Algorithmica. 1997.
12 William S.Klug and Michael R.Cummings, Genetics. Sixth Edition, pp. 251-281.
13 Uwe Ohler, Promoter Prediction on a Genomic scale-the Adh Experience, Preprint from Genomes Res. 2000, pp. 539-542.
14 Mark Nelson, "Fast String Searching With Suffix Trees", Dr. Dobb's Journal, 1996.
15 Ogasawara, j. and Morishita, S. Fast and Sensitive Algorithm for Aligning Ests to Human Genome. Bioinfomatics Conference, Proceedings. IEEE Computer Society, 2002, pp. 43-53.