Algorithms in Bioinformatics

1. Front Matter

   Pages I-X

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2. Simultaneous Relevant Feature Identification and Classification in High-Dimensional Spaces

   • L. R. Grate, C. Bhattacharyya, M. I. Jordan, I. S. Mian

   Pages 1-9

3. Pooled Genomic Indexing (PGI): Mathematical Analysis and Experiment Design

   • Miklós Csűrös, Aleksandar Milosavljevic

   Pages 10-28

4. Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem

   • Romeo Rizzi, Vineet Bafna, Sorin Istrail, Giuseppe Lancia

   Pages 29-43

5. Methods for Inferring Block-Wise Ancestral History from Haploid Sequences

   • Russell Schwartz, Andrew G. Clark, Sorin Istrail

   Pages 44-59

6. Finding Signal Peptides in Human Protein Sequences Using Recurrent Neural Networks

   • Martin Reczko, Petko Fiziev, Eike Staub, Artemis Hatzigeorgiou

   Pages 60-67

7. Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass Spectrometry

   • Nathan Edwards, Ross Lippert

   Pages 68-81

8. Improved Approximation Algorithms for NMR Spectral Peak Assignment

   • Zhi-Zhong Chen, Tao Jiang, Guohui Lin, Jianjun Wen, Dong Xu, Ying Xu

   Pages 82-96

9. Efficient Methods for Inferring Tandem Duplication History

   • Louxin Zhang, Bin Ma, Lusheng Wang

   Pages 97-111

10. Genome Rearrangement Phylogeny Using Weighbor

    • Li-San Wang

    Pages 112-125

11. Segment Match Refinement and Applications

    • Aaron L. Halpern, Daniel H. Huson, Knut Reinert

    Pages 126-139

12. Extracting Common Motifs under the Levenshtein Measure: Theory and Experimentation

    • Ezekiel F. Adebiyi, Michael Kaufmann

    Pages 140-156

13. Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics

    • Michael H. Goldwasser, Kao Ming-Yang, Lu Hsueh-I

    Pages 157-171

14. FAUST: An Algorithm for Extracting Functionally Relevant Templates from Protein Structures

    • Mariusz Milik, Sandor Szalma, Krzysztof A. Olszewski

    Pages 172-184

15. Efficient Unbound Docking of Rigid Molecules

    • Dina Duhovny, Ruth Nussinov, Haim J. Wolfson

    Pages 185-200

16. A Method of Consolidating and Combining EST and mRNA Alignments to a Genome to Enumerate Supported Splice Variants

    • Raymond Wheeler

    Pages 201-209

17. A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding

    • Mihaela Pertea, Steven L. Salzberg

    Pages 210-219

18. Comparative Methods for Gene Structure Prediction in Homologous Sequences

    • Christian N.S. Pedersen, Tejs Scharling

    Pages 220-234

19. MultiProt — A Multiple Protein Structural Alignment Algorithm

    • Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson

    Pages 235-250

20. A Hybrid Scoring Function for Protein Multiple Alignment

    • Emily Rocke

    Pages 251-262

We are pleased to present the proceedings of the Second Workshop on Al- rithms in Bioinformatics (WABI 2002), which took place on September 17-21, 2002 in Rome, Italy. The WABI workshop was part of a three-conference me- ing, which, in addition to WABI, included the ESA and APPROX 2002. The three conferences are jointly called ALGO 2002, and were hosted by the F- ulty of Engineering, University of Rome “La Sapienza”. Seehttp://www.dis. uniroma1.it/˜algo02 for more details. The Workshop on Algorithms in Bioinformatics covers research in all areas of algorithmic work in bioinformatics and computational biology. The emphasis is on discrete algorithms that address important problems in molecular biology, genomics,andgenetics,thatarefoundedonsoundmodels,thatarecomputati- ally e?cient, and that have been implemented and tested in simulations and on real datasets. The goal is to present recent research results, including signi?cant work in progress, and to identify and explore directions of future research. Original research papers (including signi?cant work in progress) or sta- of-the-art surveys were solicited on all aspects of algorithms in bioinformatics, including, but not limited to: exact and approximate algorithms for genomics, genetics, sequence analysis, gene and signal recognition, alignment, molecular evolution, phylogenetics, structure determination or prediction, gene expression and gene networks, proteomics, functional genomics, and drug design.

• Alignment
• Proteomics
• Termination
• algorithms
• bioinformatics
• evolution
• gene expression
• genetics
• genome
• sequence analysis
• algorithm analysis and problem complexity
• data structures

• IMIM-UPF-CRG, Barcelona, Spain

  Roderic Guigó

• Department of Computer Science, University of California, Davis, USA

  Dan Gusfield

Policies and ethics