CLAGen: A tool for clustering and annotating gene sequences using a suffix tree algorithm

BioSystems

Volumn 84, Issue 3, 2006, Pages 175-182

  Han, Sang il ^a   Lee, Sung Gun ^a   Kim, Kyung Hoon ^a   Choi, Chung Jung ^a   Kim, Young Han ^b   Hwang, Kyu Suk ^a  

^a Pusan National University   (South Korea)

^b Dong A University   (South Korea)

Author keywords

BLAST; CLAGen; Clustering; Gene sequence; Multiple sequence alignment; TCA cycle

Indexed keywords

ALGORITHM; CLUSTER ANALYSIS; GENE;

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; DATA BASE; EVALUATION; GENE CLUSTER; GENE SEQUENCE; NUCLEOTIDE SEQUENCE; PROTEIN DATABASE;

EID: 33646126510     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2005.11.001     Document Type: Article

References (25)

1. Altschul S.F., Gish W., Miller W., Myers E., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
2. Andres K., Nikolaj B., and Soren B. PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic Acids Res. 27 1 (1999) 237-239
3. Chen J.Y., and Carlis J.V. Genomic data modeling. Inf. Syst. 28 (2003) 287
4. Delcher A.L., Kasif S., Fleischmann R.D., Peterson J., White O., and Salzberg S.L. Alignment of whole genomes. Nucleic Acids Res. 27 11 (1999) 2369-2376
5. Delcher A.L., Phillippy A., Carlton J., and Salzberg S.L. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30 11 (2002) 2478-2483
6. Gusfield D. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology (1997), Cambridge University Press, London p. 116
7. Higgins D.G., and Sharp P.M. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73 (1988) 237-244
8. Hon W.K., and Sadakane K. Space-economical algorithms for finding maximal unique matches. Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching, vol. 2373 (2002) 144-152
9. Kalyanaraman, A., Aluru, S., Kothari, S., 2002. Parallel EST clustering. HICOMB 185.
10. Karplus M., and Kuriyan J. Molecular dynamics and protein function. Natl. Acad. Sci. U.S.A. 102 19 (2005) 6679-6685
11. Kay H., Philipp B., Laurent F., and Amos B. The PROSITE database, its status in 1999. Nucleic Acids Res. 27 1 (1999) 215-219
12. Marchler-Bauer A., Anderson J.B., Cherukuri P.F., DeWeese-Scott C., Geer L.Y., Gwadz M., He S., Hurwitz D.I., Jackson J.D., Ke Z., Lanczycki C.J., Liebert C.A., Liu C., Lu F., Marchler G.H., Mullokandov M., Shoemaker B.A., Simonyan V., Song J.S., Thiessen P.A., Yamashita R.A., Yin J.J., Zhang D., and Bryant S.H. CDD: a conserved domain database for protein classification. Nucleic Acids Res. 33 (2005) 192-196
13. McCreight E. A space economical suffix tree construction algorithm. J. ACM 23 (1976) 262-272
14. Morgenstern B., Frech K., Dress A., and Werner T. DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics 14 (1998) 290-295
15. Mount D.W. Bioinformatics: Sequence and Genome Analysis (2001), Cold Spring Harbor Laboratory Press, New York pp. 3-5
16. Notredame C., and Higgins D.G. SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res. 24 (1996) 1515-1524
17. Ostell J.M., Wheelan S.J., and Kans J.A. The NCBI data model. Methods Biochem. Anal. 43 (2001) 19
18. Phillips A., Janies D., and Wheeler W. Multiple sequence alignment in phylogenetic analysis. Mol. Phylogenet. Evol. 16 (2000) 317-330
19. Smith T.F., and Waterman M.S. Identification of common molecular sequences. J. Mol. Biol. 147 (1981) 195-197
20. Thalia A.F., Gabriel W., and Jeffrey I.G. The biology and enzymology of protein N-myristoylation. JBC 276 43 (2001) 39501-39504
21. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
22. Ukkonen E. On-line construction of suffix trees. Algorithmica 14 (1995) 249-260
23. Volfovsky N., Haas B.J., and Salzberg S.L. A clustering method for repeat analysis in DNA sequences. Genome Biol. 2 (2001) 1-11
24. Zamir O., and Etzioni O. Web document clustering: a feasibility demonstration. Proceedings of SIGIR (1998) 46-54
25. Zamir O., Etzioni O., Madani O., and Karp R.M. Fast and intuitive clustering of web documents. Proceedings of the Third International Conference on Knowledge Discovery and Data Mining (1997) 287-290