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International Conference on Computational Systems-Biology and Bioinformatics

CSBio 2010: Computational Systems-Biology and Bioinformatics pp 151–164Cite as

INVERTER: INtegrated Variable numbER Tandem rEpeat findeR

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Part of the book series: Communications in Computer and Information Science ((CCIS,volume 115))

Abstract

A tandem repeat in DNA is a sequence of two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats occur in the genomes of both eukaryotic and prokaryotic organisms. They are important in numerous fields including disease diagnosis, mapping studies, human identity testing (DNA fingerprinting), sequence homology and population studies. Although tandem repeats have been used by biologists for many years, there are few tools available for performing an exhaustive search for all tandem repeats in a given sequence. In this paper, we present INVERTER, a de novo tandem repeat finder without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool. INVERTER is implemented in Java and has a built-in user-friendly Graphical User Interface. A standalone version of the program can be downloaded from http://bmserver.sce.ntu.edu.sg/INVERTER . Comparison search result of INVERTER with an existing software tool is presented. The use of INVERTER will assist biologists in discovering new ways of understanding both the structure and function of DNA and protein.

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Author information

Authors and Affiliations

  1. School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798

    Adrianto Wirawan & Chee Keong Kwoh

  2. Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Road, 119074, Singapore

    Adrianto Wirawan, Li Yang Hsu & Tse Hsien Koh

Authors
  1. Adrianto Wirawan
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  2. Chee Keong Kwoh
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  3. Li Yang Hsu
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  4. Tse Hsien Koh
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Editor information

Editors and Affiliations

  1. School of Information Technology, King Mongkut’s University of Technology Thonburi, 126 Pracha U-Thit Rd, Bangmod, Thungkru, 10140, Bangkok, Thailand

    Jonathan H. Chan

  2. School of Computer Engineering, Nanyang Technological University, Block N4, 2b-39,Nanyang Avenue, 639798, Singapore

    Yew-Soon Ong

  3. Dept. of Computer Science, Yonsei University, 134 Shinchon-dong, Sudaemoon-ku, 120-749, Seoul, South Korea

    Sung-Bae Cho

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© 2010 Springer-Verlag Berlin Heidelberg

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Wirawan, A., Kwoh, C.K., Hsu, L.Y., Koh, T.H. (2010). INVERTER: INtegrated Variable numbER Tandem rEpeat findeR. In: Chan, J.H., Ong, YS., Cho, SB. (eds) Computational Systems-Biology and Bioinformatics. CSBio 2010. Communications in Computer and Information Science, vol 115. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16750-8_14

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  • DOI: https://doi.org/10.1007/978-3-642-16750-8_14

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-16749-2

  • Online ISBN: 978-3-642-16750-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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