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RCA-mer: A Web-Based Program Searching for Primer Candidates  

Cho, Young-Hoon (Department of Bioinformatics, Korea Bio Polytechnic)
Park, Kie-Jung (Information Technology Institute, SmallSoft Co. Ltd.)
Lee, Dae-Sang (Department of Bioinformatics, Korea Bio Polytechnic)
Publication Information
Korean Journal of Microbiology / v.44, no.2, 2008 , pp. 164-167 More about this Journal
Abstract
Recently, rolling circle amplification (RCA) technique has been widely focused in the field of gene amplification just like PCR method. We have developed RCA-mer, which is a web-based program searching for primer candidates from a given sequence. It can be applied to find primer lists in DNA amplification experiment based on RCA method. The RCA-mer compares 8-mer primer lists with user's input sequence such as vector, mitochondria, and microbial genome sequence. After calculating 8-mers existences in a given sequence, it displays matched and no-matched primer lists with their GC-contents. In addition to it, RCA-mer can search the existence of 8-mer primer lists in two sequences whether they are co-existed or not. Users can apply candidate primer lists to their researches which use RCA techniques.
Keywords
Fosmid; N-mer; PCR; primer; rolling circle amplification; vector;
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Times Cited By KSCI : 1  (Citation Analysis)
Times Cited By SCOPUS : 0
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1 이대상, 박기정. 2007. 미생물 유전체 프로젝트 수행을 위한 Base-Calling 오류감지 프로그램 및 알고리즘 개발. 한국미생물학회지 43, 317-320   과학기술학회마을
2 Liu, D., S.L. Daubendiek, M.A. Zillman, K. Ryan, and E.T. Kool. 1996. Rolling circle DNA synthesis: Small circular oligonucleotides as efficient templates for DNA polymerases. J. Am. Chem. Soc. 118, 1587-1594   DOI   ScienceOn
3 Kingsmore, S.F. and D.D. Patel. 2003. Multiplexed protein profiling on antibody-based microarrays by rolling circle amplification. Curr. Opin. Biotechnol. 14, 74-81   DOI   ScienceOn
4 Alsmadi, O.A., C.J. Bornarth, W. Song, M. Wisniewski, J. Du, J.P. Brockman, A.F. Faruqi, S. Hosono, Z. Sun, Y. Du, X. Wu, M. Egholm, P. Abarzua, R.S. Lasken, and M.D. Driscoll. 2003. High accuracy genotyping directly from genomic DNA using a rolling circle amplification based assay. BMC Genomics 4, 1471-2164
5 Fire, A. and S.Q. Xu. 1995. Rolling replication of short DNA circles. Proc. Natl. Acad. Sci. USA 92, 4641-4645   DOI
6 이대상, 태홍석, 박기정. 2003. 유전정보분석시스템. 전자공학회지 30, 68-78
7 Dean, F.B., J.R. Nelson, T.L. Giesler, and R.S. Lasken. 2001. Polymerase and multiply-primed rolling circle amplification. Genome Res. 11, 1095-1099   DOI   ScienceOn
8 Fumito, M., K. Takehiko, Y. Nobuyasu, T. Katsuji, and N. Masao. 2005. Visualization and enumeration of bacteria carrying a specific gene sequence by in situ rolling circle amplification. Appl. Environ. Microbiol. 71, 7933-7940   DOI   ScienceOn