INVERTER: INtegrated Variable numbER Tandem rEpeat findeR

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.