approximate nested tandem repeat
(NTR) in a string
is a complex repetitive structure consisting of many approximate copies of two substrings
(“motifs”) interspersed with one another. NTRs have been found in real DNA sequences and are expected to have applications for evolutionary studies, both as a tool to understand concerted evolution, and as a potential marker in population studies.
In this paper we describe software tools developed for database searches for NTRs. After a first program
identifies putative NTR motifs, a confirmation step requires the application of the alignment of the putative NTR against exact NTRs built from the putative template motifs
. In this paper we describe an algorithm to solve this alignment problem in
x| + |
space and time. Our alignment algorithm is based on Fischetti et al.’s wrap-around dynamic programming.