Abstract
An approximate nested tandem repeat (NTR) in a string T is a complex repetitive structure consisting of many approximate copies of two substrings x and X (“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 NTRFinder 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 x and X. In this paper we describe an algorithm to solve this alignment problem in O(|T|(| x| + | X|)) space and time. Our alignment algorithm is based on Fischetti et al.’s wrap-around dynamic programming.
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Matroud, A.A., Hendy, M.D., Tuffley, C.P. (2010). An Algorithm to Solve the Motif Alignment Problem for Approximate Nested Tandem Repeats. In: Tannier, E. (eds) Comparative Genomics. RECOMB-CG 2010. Lecture Notes in Computer Science(), vol 6398. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16181-0_16
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DOI: https://doi.org/10.1007/978-3-642-16181-0_16
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