Algorithms in Bioinformatics - Info and Reading Options

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Intro -- Title Page -- Preface -- Conference Organization -- Table of Contents -- Multichromosomal Genome Median and Halving Problems -- Introduction -- Genomes, Breakpoints and Rearrangements -- Computational Problems -- Breakpoint Distance, General Case -- Breakpoint Distance, Linear Case -- DCJ Distance, General Case -- DCJ and Reversal/Translocation, Linear Chromosomes -- Conclusions -- References -- A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem -- Introduction -- Background and Notions -- Genome Rearrangements -- Genomic Distance for Multichromosomal Genomes -- Reversal Median Problem -- Graph Model for Undirected Genome -- Capless Breakpoint Graph -- Lower Bound of the HP Distance -- Contraction Operation -- Branch-and-Bound Algorithm -- A Basic Branch-and-Bound Algorithm for PMP -- Genome Enumeration -- Improved Branch-and-Bound Algorithm for PMP -- Branch-and-Bound Algorithm for RMP -- Experimental Results -- Conclusions -- References -- Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions -- Introduction -- Graph and Subgraph Structures -- Breakpoint Graph -- Multiple Breakpoint Graph and Median Graph -- MBG Subgraphs and Connecting Edges -- Crossing Edges and Decomposers -- Adequate and Strongly Adequate Subgraphs -- Edge Shrinking, Expansion and Contraction -- An Adequate Subgraph Is a Decomposer -- Median Calculation Incorporating MBG Decomposition -- Experimental Results -- The Effects of n and \pi=\rho/n on the Proportion of Rapidly Solvable Instances -- The Effect of Adequate Subgraph Discovery on Speed-Up -- Time to Solution -- Conclusion -- References -- Read Mapping Algorithms for Single Molecule Sequencing Data -- Introduction -- Algorithms -- Alignment with Weighted Sequence Graphs -- Alignment of Read Pairs with WSG -- Seeded Alignment Approach for SMS Reads

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