Gary Benson

Tandem repeats finder: a program to analyze DNA sequences

A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of re...

A method for fast database search for all<i>k</i>-nucleotide repeats

A significant portion of DNA consists of repeating patterns of various sizes, from very small (one, two and three nucleotides) to very large (over 300 nucleotides). Although the...

Sequence Alignment with Tandem Duplication

Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modification of seq...

A space efficient algorithm for finding the best nonoverlapping alignment score

On the Distribution of<i>K</i>-tuple Matches for Sequence Homology: A Constant Time Exact Calculation of the Variance

We study the distribution of a statistic useful in calculating the significance of the number of k-tuple matches detected in biological sequence homology algorithms. The statist...