Algorithms in Bioinformatics

Third International Workshop, WABI 2003, Budapest, Hungary, September 15-20, 2003, Proceedings

By: Gary Benson (Editor), Roderic Page (Editor)

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Paperback | 9 September 2003

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We are pleased to present the proceedings of the Third Workshop on Algorithms in Bioinformatics (WABI 2003), which took place on September 15-20, 2003 in Budapest, Hungary. The WABI workshop was part of the four-conference meeting, ALGO 2003, which was locally organized by Dr. Jan ´ os Csirik, Head of the Department of Computer Science, J´ ozsef Attila University, Budapest. See http://www. conferences. hu/ALGO2003/algo_2003. htmfor more details. WABI focuses on discrete algorithms that address important problems in molecular biology, genomics, and genetics, that are founded on sound models, that are computationally e?cient, that have been implemented and tested in simulations and on real datasets, and that provide new biological results. The workshopgoalsareto presentrecentresearchandidentify andexploredirections for future research. We received78 submissionsin responseto the call for papers and 36 were- cepted. We wouldliketo sincerelythank the authorsof allsubmitted papers and the conference participants. We especially thank a terri?c program committee for their diligent and thorough work in reviewing and selecting the papers.

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Non-Fiction Mathematics Algebra Computing & I.T.Computer Science Science Biology, Life Sciences Biochemistry Computer Programming & Software Development Algorithms & Data Structures Graphical & Digital Media Applications 3D Graphics & Modelling

Databases Data Capture & Analysis Life Sciences in General

A Local Chaining Algorithm and Its Applications in Comparative Genomics	p. 1
Common Intervals of Two Sequences	p. 17
A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoring	p. 25
Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specificity	p. 39
A Stochastic Approach to Count RNA Molecules Using DNA Sequencing Methods	p. 55
A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence	p. 63
Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency	p. 78
New Algorithm for the Simplified Partial Digest Problem	p. 95
Noisy Data Make the Partial Digest Problem NP-hard	p. 111
Pattern Discovery Allowing Wild-Cards, Substitution Matrices, and Multiple Score Functions	p. 124
A Combinatorial Approach to Automatic Discovery of Cluster-Patterns	p. 139
Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology	p. 151
Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees	p. 165
Efficient Generation of Uniform Samples from Phylogenetic Trees	p. 177
New Efficient Algorithm for Detection of Horizontal Gene Transfer Events	p. 190
Ancestral Maximum Likelihood of Evolutionary Trees Is Hard	p. 202
A Linear-Time Majority Tree Algorithm	p. 216
Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model	p. 228
Better Hill-Climbing Searches for Parsimony	p. 245
Computing Refined Buneman Trees in Cubic Time	p. 259
Distance Corrections on Recombinant Sequences	p. 271
Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks	p. 287
Identifying Blocks and Sub-populations in Noisy SNP Data	p. 303
Designing Optimally Multiplexed SNP Genotyping Assays	p. 320
Minimum Recombinant Haplotype Configuration on Tree Pedigrees	p. 339
Efficient Energy Computation for Monte Carlo Simulation of Proteins	p. 354
Speedup LP Approach to Protein Threading via Graph Reduction	p. 374
Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment	p. 389
Side-Chain Structure Prediction Based on Dead-End Elimination: Single Split DEE-criterion Implementation and Elimination Power	p. 402
A Large Version of the Small Parsimony Problem	p. 417
Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree	p. 433
Composition Alignment	p. 447
Match Chaining Algorithms for cDNA Mapping	p. 462
Sequencing from Compomers: Using Mass Spectrometry for DNA De-Novo Sequencing of 200+ nt	p. 476
Bounds for Resequencing by Hybridization	p. 498
Selecting Degenerate Multiple PCR Primers	p. 512
Author Index	p. 527
Table of Contents provided by Blackwell. All Rights Reserved.

Algorithms in Bioinformatics

Third International Workshop, WABI 2003, Budapest, Hungary, September 15-20, 2003, Proceedings

At a Glance

Paperback

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