RISO is a software to extract conserved regions that occur in a well-ordered and regularly spaced manner in a set of DNA sequences.
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Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira and Marie-France Sagot,
An efficient algorithm for the identification of structured motifs in DNA promoter sequences,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(2):126-140, Apr-Jun, 2006.