Algorithms in Bioinformatics

1. Front Matter

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2. QCluster: Extending Alignment-Free Measures with Quality Values for Reads Clustering

   • Matteo Comin, Andrea Leoni, Michele Schimd

   Pages 1-13

3. Improved Approximation for the Maximum Duo-Preservation String Mapping Problem

   • Nicolas Boria, Adam Kurpisz, Samuli Leppänen, Monaldo Mastrolilli

   Pages 14-25

4. A Faster 1.375-Approximation Algorithm for Sorting by Transpositions

   • Luís Felipe I. Cunha, Luis Antonio B. Kowada, Rodrigo de A. Hausen, Celina M. H. de Figueiredo

   Pages 26-37

5. A Generalized Cost Model for DCJ-Indel Sorting

   • Phillip E. C. Compeau

   Pages 38-51

6. Efficient Local Alignment Discovery amongst Noisy Long Reads

   • Gene Myers

   Pages 52-67

7. Efficient Indexed Alignment of Contigs to Optical Maps

   • Martin D. Muggli, Simon J. Puglisi, Christina Boucher

   Pages 68-81

8. Navigating in a Sea of Repeats in RNA-seq without Drowning

   • Gustavo Sacomoto, Blerina Sinaimeri, Camille Marchet, Vincent Miele, Marie-France Sagot, Vincent Lacroix

   Pages 82-96

9. Linearization of Median Genomes under DCJ

   • Shuai Jiang, Max A. Alekseyev

   Pages 97-106

10. An LP-Rounding Algorithm for Degenerate Primer Design

    • Yu-Ting Huang, Marek Chrobak

    Pages 107-121

11. GAML: Genome Assembly by Maximum Likelihood

    • Vladimír Boža, Broňa Brejová, Tomáš Vinař

    Pages 122-134

12. A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems

    • Sebastian Will, Peter F. Stadler

    Pages 135-147

13. Entropic Profiles, Maximal Motifs and the Discovery of Significant Repetitions in Genomic Sequences

    • Laxmi Parida, Cinzia Pizzi, Simona E. Rombo

    Pages 148-160

14. Estimating Evolutionary Distances from Spaced-Word Matches

    • Burkhard Morgenstern, Binyao Zhu, Sebastian Horwege, Chris-André Leimeister

    Pages 161-173

15. On the Family-Free DCJ Distance

    • Fábio V. Martinez, Pedro Feijão, Marília D. V. Braga, Jens Stoye

    Pages 174-186

16. New Algorithms for Computing Phylogenetic Biodiversity

    • Constantinos Tsirogiannis, Brody Sandel, Adrija Kalvisa

    Pages 187-203

17. The Divisible Load Balance Problem and Its Application to Phylogenetic Inference

    • Kassian Kobert, Tomáš Flouri, Andre Aberer, Alexandros Stamatakis

    Pages 204-216

18. Multiple Mass Spectrometry Fragmentation Trees Revisited: Boosting Performance and Quality

    • Kerstin Scheubert, Franziska Hufsky, Sebastian Böcker

    Pages 217-231

19. An Online Peak Extraction Algorithm for Ion Mobility Spectrometry Data

    • Dominik Kopczynski, Sven Rahmann

    Pages 232-246

20. Best-Fit in Linear Time for Non-generative Population Simulation

    • Niina Haiminen, Claude Lebreton, Laxmi Parida

    Pages 247-262

This book constitutes the refereed proceedings of the 14th International Workshop on Algorithms in Bioinformatics, WABI 2014, held in Wroclaw, Poland, in September 2014. WABI 2014 was one of seven conferences that were organized as part of ALGO 2014. WABI is an annual conference series on all aspects of algorithms and data structure in molecular biology, genomics and phylogeny data analysis. The 26 full papers presented together with a short abstract were carefully reviewed and selected from 61 submissions. The selected papers cover a wide range of topics from sequence and genome analysis through phylogeny reconstruction and networks to mass spectrometry data analysis.

• bioinformatics
• complexity
• computational genomics
• data mining
• data structures
• design and analysis of algorithms
• discrete mathematics
• evolutionary dynamics
• genome assembly
• genomic sequences
• graph theory
• algorithm analysis and problem complexity

• David R. Cheriton School of Computer Science, University of Waterloo, Canada

  Dan Brown

• Institute of Microbiology and Genetics, Department of Bioinformatics, University of Göttingen, Germany, Göttingen, Germany

  Burkhard Morgenstern

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