Tandem cyclic alignment Original Research Article

We present a solution for the following problem. Given two sequences image and image, image, find the best scoring alignment of image vs. image over all possible pairs image, for image and image, where image is the cyclic permutation of image starting at image, image is the concatenation of image complete copies of image (image tandem copies), and the alignment must include all of image and all of image. Our algorithm allows any alignment scoring scheme with additive gap costs and uses image time and image space. We use it to identify related tandem repeats in the C. elegans genome as part of the development of a multi-genome database of tandem repeats.