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SNPchaser : A Web-based Program for Detecting SNPs Substitution and Heterozygosity Existence  

Jang, Jin-Woo (Department of Bioinformatics, Korea Bio Polytechnic College)
Lee, Hyun-Chul (D&P BioTech, Ltd.)
Lee, Myung-Hoon (D&P BioTech, Ltd.)
Choi, Yeon-Shik (Department of Laboratory Animals, Korea Bio Polytechnic College)
Choo, Dong-Won (Department of Bioinformatics, Korea Bio Polytechnic College)
Park, Kie-Jung (Information Technology Institute, SmallSoft Co. Ltd.)
Lee, Dae-Sang (Department of Bioinformatics, Korea Bio Polytechnic College)
Publication Information
KSBB Journal / v.24, no.4, 2009 , pp. 410-414 More about this Journal
Abstract
Single-nucleotide polymorphisms (SNPs) are the DNA sequences difference among the same species in the level of nucleic acids and are widely applied in clinical fields such as personalized medicine. The routine and labor-intensive methods to determine SNPs are performing the sequence homology search by using BLAST and navigating the trace of chromatogram files generated by high-throughput DNA sequencing machine by using Chromas program. In this paper, we developed SNPchaser, a web-based program for detecting SNPs substitution and heterozygosity existence, to improve the labor-intensive method in determining SNPs. SNPchaser performed sequence alignment and visualized the suspected region of SNPs by using user's reference sequence, AB1 files, and positional information of SNPs. It simultaneously provided the results of sequences alignment and chromatogram of relevant area of SNPs to user. In addition, SNPchaser can easily determine existence of heterozygosity in SNPs area. SNPchaser is freely accessible via the web site http://www.bioinformatics.ac.kr/SNPchaser and the source codes are available for academic research purpose.
Keywords
AB1; Alignment; Chromatogram; Heterozygosity; Sequence; SNPs;
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Times Cited By KSCI : 1  (Citation Analysis)
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