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.
INVERTER is 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. INVERTER is aimed to identify both exact match and non-exact match VNTRs and provide data visualization which would allow users to correlate annotations, observe visual patterns, and view useful statistics of the data. More specifically, INVERTER is more optimized towards minisatellite VNTRs. The visualization tool is aimed to provide data visualization of the resulting VNTRs, which would allow users to correlate annotations, observe visual patterns, and view useful statistics of the data. The visualization tool includes four features, i.e. table view, zoom view, statistics and intra-inter repeat.
- Kian Guan Lim, Chee Keong Kwoh, Adrianto Wirawan, Li Yang Hsu: "Review of Tandem Repeat Search Tools: A Systematic Approach to Evaluating Algorithmic Performance." Briefings in Bioinformatics, 2012, accepted
- Adrianto Wirawan, Chee Keong Kwoh, Li Yang Hsu, Tse Hsien Koh: "INVERTER: INtegrated Variable numbER Tandem rEpeat findeR." Communications in Computer and Information Science, 2010, 115, (4): 151-164