Automatically Predicting Possible Loci of Variable Number of Tandem Repeats.
Journal
4th IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2004), 19-21 March 2004, Taichung, Taiwan
Pages
475-482
Date Issued
2004
Author(s)
Chang, Chia-Hung
Chuang, Han-Yu
Chiang, Yi-Hung
Chiou, Chien-Shun
Lu, Hsueh-I
Kao, Cheng-Yan
HSUEH-I LU
Abstract
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.
Type
conference paper