Browse > Article
http://dx.doi.org/10.5391/JKIIS.2004.14.5.545

Web-based Research Assistant Tools for Analysis of Microbial Diversity  

Kang, Byeong-Chul (동서대학교 응용생명공학부, 부산대학교 의과대학부설 부산지놈센터)
Kim, Hyun-Jin (부산대학교 대학원 생물정보학협동과)
Park, Jun-Hyung (부산대학교 대학원 생물정보학협동과정, 부산대학교 의과대학부설 부산지놈센)
Park, Hee-Kyung (부산대학교 의과대학 생화학교)
Kim, Cheol-Min (부산대학교 대학원 생물정보학협동과정, 부산대학교 의과대학부설 부산지놈센터. 부산대학교 의과대학 생화학교실)
Publication Information
Journal of the Korean Institute of Intelligent Systems / v.14, no.5, 2004 , pp. 545-550 More about this Journal
Abstract
The study of available genotypes (biodiversity analysis) in bacterial communities is of growing importance in several fields such as ecology, environmental technology, clinical diagnostics, etc. These culture-independent genotyping techniques, especially amplifying 16S rRNA genes, attempt to overcome some shortcomings of conventional cultivation method. Biodiversity analysis based on molecular technique were laborious for base-calling chromatogram, trimming primer sites, correcting strand directions, electing representative operation taxonomic units (OTU), etc. Also, biologists wanted intuitively to confirm results of the above processes. For making up these demands, we developed the web application based on Folder-Process-Filter (FPF) modeling with correspondence to classical Model-View-Controller model. The model of web application leads to keep virtues of simplicity and directness for development and management of the stepwise web interfaces. The web application was developed in Perl and CGI on Linux workstation. It can be freely accessed from http://home.pusan.ac.kr/～genome/tools/rat.htm.
Keywords
생물다양성분석;생물정보학;핵산염기서열분석;웹 어플리케이션 객체모델링;객체지향모델링;
Citations & Related Records
연도 인용수 순위
  • Reference
1 N.P. Brown, C. Leroy, and C. Sander, "MView: A Web compatible database search or multiple alignment viewer," Bioinformatics, Vol. 14, pp. 380-381 1998.   DOI   ScienceOn
2 J.R. Cole, B. Chai, T.L. Marsh, R.J. Farris,Q. Wang, S.A. Kulam, S. Chandra, D.M. McGarrell, T.M. Schmidt, G.M. Garrity, and J.M. Tiedje, "The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy," Nucleic Acids Res., Vol. 31, pp. 442-443, 2003.   DOI   ScienceOn
3 J. Felsenstein, PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author, Department of Genetics, University of Washington, Seattle, 1993.
4 D. Frishman, K. Albermann, J. Hani, K. Heumann, A. Metanomski, A. Zollner, H.W. Mewes, "Functional and structural genomics using PEDANT," Bioinformatics, Vol. 17, pp. 44-57, 2001.   DOI   ScienceOn
5 J.E. Stajich, D. Block, K. Boulez, S.E. Brenner, S.A. Chervitz, C. Dagdigian, G. Fuellen, J.G.R. Gilbert, I. Korf, H. Lapp, H. Lehvaslaiho, C. Matsalla, C.J. Mungall, B.I. Osborne, M.R. Pocock, P. Schattner, M. Senger, L.D. Stein, E.D. Stupka, M. Wilkinson, and E. Birney, "The Bioperl Toolkit: Perl modules for the life sciences," Genome Research, Vol. 12, pp. 1161-1168, 2002.
6 C.A. Letondal, "Web interface generator for molecular biology programs in Unix," Bioinformatics., Vol. 17, pp. 73-82, 2001.   DOI   ScienceOn
7 J. Erlbaum, http://search.cpan.org/~markstos/CGI- Application-3.22/lib/CGI/Application.pm
8 A. Wardley, http://search.cpan.org/~abw/Template- Toolkit-2.13/lib/Template.pm
9 S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman, "A basic local alignment search tool," Journal of Molecular Biology, Vol. 215, pp. 403-410, 1990.   DOI
10 J.D. Thompson, D.G. Higgins, and T.J. Gibson, "CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice," Nucleic Acids Res., Vol. 22, pp. 4673, 1994.   DOI   ScienceOn
11 W. Ludwig, O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Förster, I. Brettske, S. Gerber, A.W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. König, T. Liss, R. Lüßmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K-H. Schleifer, "ARB: a software environment for sequence data," Nucleic Acids Res., Vol. 32(4), pp. 1363-1371, 2004.   DOI   ScienceOn
12 I. Dahllof, "Molecular community analysis of microbial diversity," Curr. Opin. Biotechnol., Vol. 13, pp. 213-217, 2002.   DOI   ScienceOn
13 D.M Olive, and P. Bean, "Principles and Applications of Methods for DNA-Based Typing of Microbial Organisms," J. of Clin. Microbiol., Vol. 37, pp. 1661-1669, 1999.
14 B. Pace, and L.L Campbell, "Homology of ribosomal ribonucleic acid of diverse bacterial species with Escherichia coli and Bacillus stearothermophilus," J. Bacteriol., Vol. 107, pp. 543-547, 1971.
15 SVG, http://www.adobe.com/svg/main.html