Algorithms in Bioinformatics: 16th International Workshop, by Martin Frith, Christian Nørgaard Storm Pedersen

By Martin Frith, Christian Nørgaard Storm Pedersen

This ebook constitutes the refereed complaints of the sixteenth overseas Workshop on Algorithms in Bioinformatics, WABI 2016, held in Aarhus, Denmark. The 25 complete papers  together with 2 invited talks offered have been rigorously reviewed and chosen from fifty four submissions.

The chosen papers disguise quite a lot of themes from networks, to
phylogenetic reports, series and genome research, comparative genomics, and mass spectrometry info analysis. 

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Read or Download Algorithms in Bioinformatics: 16th International Workshop, WABI 2016, Aarhus, Denmark, August 22-24, 2016. Proceedings (Lecture Notes in Computer Science) PDF

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Extra resources for Algorithms in Bioinformatics: 16th International Workshop, WABI 2016, Aarhus, Denmark, August 22-24, 2016. Proceedings (Lecture Notes in Computer Science)

Example text

For 1 ≤ i ≤ j ≤ |S|, we let S[i, j] = σi · · · σj denote the interval of S beginning at position i and ending at position j. We call a sequence where all characters are different a permutation. Two sequences S1 and S2 are said to be equivalent, denoted S1 ≡ S2 , if |{S1 [i] = σ : 1 ≤ i ≤ |S1 |}| = |{S2 [i] = σ : 1 ≤ i ≤ |S2 |}| for all σ ∈ Σ. In other words, S1 ≡ S2 if both sequences have the same number of occurrences of each character σ ∈ Σ. Clearly, for two equivalent sequences S1 and S2 we have |S1 | = |S2 |.

Keywords: Cancer mutations optimization · Network analysis 1 · Branch and cut · Combinatorial Introduction Recent advances in DNA sequencing technologies have allowed the study of cancer genomes at an unprecedented level of detail. In particular, it is now possible to measure all somatic mutations, changes in the DNA arising during the lifetime of an individual and causing the disease, in a large number of cancer patients [12,28]. These large cancer studies have shown that each individual tumour harbours hundreds or thousands somatic mutations, with two tumours showing a large diversity in the complement of somatic mutations they exhibit [9,27].

Tik } satisfying: 1. 2. 3. 4. q is a subsequence of some interval of length d in Q, tij is a subsequence of some interval in Iij for each 1 ≤ j ≤ k, i1 = i2 = · · · = ik , and q ≡ tij for each 1 ≤ j ≤ k. We say that a block {q, ti1 , . . , tik } is maximal in (Q, I, d) if there is no other block {q , tj1 , . . , tj } in this instance where q is a subsequence of q and {i1 , . . , ik } ⊆ {j1 , . . , j }. Definition 2 (Reference Anchored Gene Blocks Problem (RAGB)). The Reference Anchored Gene Blocks problem is the problem of computing all maximal blocks in a given problem instance (Q, I, d).

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