In this paper, we study the problem of efficiently finding gene clusters formalized by nested common intervals between two genomes represented either as permutations or as sequences. Considering permutations, we give several algorithms whose running time depends on the size of the actual output rather than the output in the worst case. Indeed, we first provide a straightforward O(n3) time algorithm for finding all nested common intervals. We reduce this complexity by providing an O(n2) time algorithm computing an irredundant output. Finally, we show, by providing a third algorithm, that finding only the maximal nested common intervals can be done in linear time. Considering sequences, we provide solutions (modifications of previously defined algorithms and a new algorithm) for different variants of the problem, depending on the treatment one wants to apply to duplicated genes. © 2009 Springer-Verlag Berlin Heidelberg.
CITATION STYLE
Blin, G., & Stoye, J. (2009). Finding nested common intervals efficiently. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 5817 LNBI, pp. 59–69). https://doi.org/10.1007/978-3-642-04744-2_6
Mendeley helps you to discover research relevant for your work.