Abstract
We examine the problem of finding maximal-scoring sets of disjoint regions in a sequence of scores. The problem arises in DNA and protein segmentation, and in post-processing of sequence alignments. Our key result states a simple recursive relationship between maximal-scoring segment sets. The statement leads to an algorithm that finds such a k-set of segments in a sequence of length n in O(nk) time. We describe linear-time algorithms for finding optimal segment sets using different criteria for choosing k, as well as an algorithm for finding an optimal set of k segments in O(nlog n) time, independently of k. We apply our methods to the identification of non-coding RNA genes in thermophiles.
Work supported by NSERC grant 250391-02.
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Csűrös, M. (2004). Algorithms for Finding Maximal-Scoring Segment Sets. In: Jonassen, I., Kim, J. (eds) Algorithms in Bioinformatics. WABI 2004. Lecture Notes in Computer Science(), vol 3240. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30219-3_6
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DOI: https://doi.org/10.1007/978-3-540-30219-3_6
Publisher Name: Springer, Berlin, Heidelberg
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