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Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04)
Automatically Predicting Possible Loci of Variable Number of Tandem Repeats
Taichung, Taiwan, ROC
May 19-May 21
ISBN: 0-7695-2173-8
Chia-Hung Chang, National Taiwan University, Taipei
Han-Yu Chuang, National Taiwan University, Taipei
Yi-Hung Chiang, National Taiwan University, Taipei
Chien-Shun Chiou, Center for Disease Control, Taiwan
Hsueh-I Lu, Academia Sinica, Taipei, Taiwan
Cheng-Yan Kao, National Taiwan University, Taipei
Variable number of tandem repeats (VNTR) stands for a tandem repeat which has variation in length and the number of repeated segments between individuals. VNTRs are useful as molecule markers in many applications, such as DNA fingerprinting, genetic disease analysis and molecular typing of prokaryotes. It costs a large amount of money and time to identify these special loci by using traditional biological experiments. Here we develop a novel tool, VNTR analyzer, to identify and analyze VNTR in genome sequence by comparing genomic sequences of different strains. In this study, we demonstrate its ability to detect VNTRs by analyzing 3 bacterial species: Staphylococcus aureus, Xylella fastidiosa and Salmonella enterica. The results showed that our program could find VNTRs accurately in a short time. Moreover, the program provides biologists a colorful visualization tool for further analysis.
Citation:
Chia-Hung Chang, Han-Yu Chuang, Yi-Hung Chiang, Chien-Shun Chiou, Hsueh-I Lu, Cheng-Yan Kao, "Automatically Predicting Possible Loci of Variable Number of Tandem Repeats," bibe, pp.475, Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04), 2004
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