Software
TRedD - Tandem Repeats Software - Funded by the NSF grant DB&I 0542751, we have developed software for locating tandem repeats, TRed, and a database of tandem repeats in the human genome, TRedD.
Finding General Repeats via Smith-Waterman An online interface, in conjuction with our DIMACS Educational Module, to illustrate the SW algorithm for finding repeats in an input sequence.
TandemGraph This graphical tool was developed in java for modeling tandem repeats in a chromosome.
Dictionary Matching Software We developed 1D dictionary matching using small space with the compressed suffix tree as the underlying data structure.
Suffix Tree Construction: Developed software in Java for constructing a suffix tree and a generalized suffix tree based on Ukkonen’s algorithm.
Clustering Tandem Repeats Developed software in R and perl for clustering and classification of tandem repeats in the human genome.