Bioinformatics Research and Applications: Fourth by Dan L. Nicolae, Omar De la Cruz, William Wen (auth.), Ion

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By Dan L. Nicolae, Omar De la Cruz, William Wen (auth.), Ion Măndoiu, Raj Sunderraman, Alexander Zelikovsky (eds.)

This e-book constitutes the refereed court cases of the Fourth overseas Symposium on Bioinformatics learn and purposes, ISBRA 2008, held in Atlanta, GA, united states in may perhaps 2008.

The 35 revised complete papers provided including 6 workshop papers and six invited papers have been rigorously reviewed and chosen from a complete of ninety four submissions. The papers conceal a variety of issues, together with clustering and class, gene expression research, gene networks, genome research, motif discovering, pathways, protein constitution prediction, protein area interactions, phylogenetics, and software program tools.

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Additional info for Bioinformatics Research and Applications: Fourth International Symposium, ISBRA 2008, Atlanta, GA, USA, May 6-9, 2008. Proceedings

Example text

Theorem 1. Algorithm 1 solves the 2–NNI–Search problem in O(rmn) time. Proof. (Correctness) Each tree T ∈ 2 − NNIS belongs to one of the following cases: 1. T ∈ NNIS : The tree T1 computed in Algorithm 1 is a tree with minimum reconciliation cost among all trees in NNIS . 2. T ∈ 2 − NNIS \ NNIS : There exist two nodes s, t ∈ V (S) such that T = NNIT (t), and T = NNIS (s). We now have two possible cases: (a) t ∈ indS (s): According to Lemma 6, the tree T2 computed by Algorithm 1 must be a minimum reconciliation cost tree among all trees in this case.

Springer, Heidelberg (2005) 15. : Reconstruction of ancient molecular phylogeny. Molecular Phylogenetics and Evolution 6(2), 189–213 (1996) 16. : New algorithms for the duplication-loss model. In: RECOMB, pp. 138–146 (2000) 17. : From gene trees to species trees. SIAM J. Comput. 30(3), 729–752 (2000) 18. : A biology consistent model for comparing molecular phylogenies. Journal of Computational Biology 2(4), 493–507 (1995) 19. : Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas.

Eulenstein Definition 2 (Comparability). The trees G and S are comparable if there exists a leaf-mapping LG,S . A set of gene trees G and S are comparable if each gene tree in G is comparable with S. Throughout this paper we use the following terminology: G is a set of gene trees that is comparable with a species tree S, and G ∈ G. Definition 3 (Duplication). A node v ∈ V (G) is a (gene) duplication if MG,S (v) ∈ MG,S (Ch(v)) and we define Dup(G, S) = {g ∈ V (G) : g is a duplication}. Definition 4 (Reconciliation cost).

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