Titlebook: Algorithms in Bioinformatics; 4th International Wo Inge Jonassen,Junhyong Kim Conference proceedings 2004 Springer-Verlag Berlin Heidelberg

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Sorting by Reversals with Common Intervalsn allowed reversals. We do not allow to break conserved clusters of genes usually called Common Intervals. We show that this problem is NP-complete. Assuming special conditions, we propose a polynomial algorithm..Omitted proofs are given as supplementary material at .

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Gapped Local Similarity Search with Provable Guaranteesnder certain reasonable input assumptions. Our . program has provable sensitivity (even on worst-case inputs) and average-case performance guarantees. It is significantly faster than a fully sensitive dynamic-programming-based program for strong similarity search on longsequences.

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Algorithms for Finding Maximal-Scoring Segment Setsoptimal segment sets using different criteria for choosing ., as well as an algorithm for finding an optimal set of . segments in .(.log .) time, independently of .. We apply our methods to the identification of non-coding RNA genes in thermophiles.

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Adding Hidden Nodes to Gene Networkss expansion, show it is hard, and describe an EM based heuristic algorithm for solving it. The algorithm was applied to synthetic datasets and to yeast gene expression datasets, and produces good, encouraging results.