Algorithms in Bioinformatics: 7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings

The refereed proceedings from the 7th International Workshop on Algorithms in Bioinformatics are provided in this volume. Papers address current issues in algorithms in bioinformatics, ranging from mathematical tools to experimental studies of approximation algorithms to significant computational analyses. Biological problems examined include genetic mapping, sequence alignment and analysis, phylogeny, comparative genomics, and protein structure.

Table of Contents:
Shotgun Protein Sequencing.- Locality Kernels for Protein Classification.- When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features.- Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps.- Bringing Folding Pathways into Strand Pairing Prediction.- A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage.- Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies.- Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity.- Haplotype Inference Via Hierarchical Genotype Parsing.- Seeded Tree Alignment and Planar Tanglegram Layout.- Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion.- An ?(n 2/logn) Speed-Up of Heuristics for the Gene-Duplication Problem.- Incremental Discovery of Irredundant Motif Bases in Time O(|?|n 2 logn).- A Graph Clustering Approach to Weak Motif Recognition.- Informative Motifs in Protein Family Alignments.- Topology Independent Protein Structural Alignment.- Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for Protein Structure Prediction.- Alignment-Free Local Structural Search by Writhe Decomposition.- Defining and Computing Optimum RMSD for Gapped Multiple Structure Alignment.- Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding.- Genomic Signatures in De Bruijn Chains.- Fast Kernel Methods for SVM Sequence Classifiers.- On-Line Viterbi Algorithm for Analysis of Long Biological Sequences.- Predicting Protein Folding Kinetics Via Temporal Logic Model Checking.- Efficient Algorithms to Explore Conformation Spaces of Flexible ProteinLoops.- Algorithms for the Extraction of Synteny Blocks from Comparative Maps.- Computability of Models for Sequence Assembly.- Fast Algorithms for Selecting Specific siRNA in Complete mRNA Data.- RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound.- HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding.- Homology Search with Fragmented Nucleic Acid Sequence Patterns.- Fast Computation of Good Multiple Spaced Seeds.- Inverse Sequence Alignment from Partial Examples.- Novel Approaches in Psychiatric Genomics.- The Point Placement Problem on a Line – Improved Bounds for Pairwise Distance Queries.- Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach.- Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data.- A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence.- Composing Globally Consistent Pathway Parameter Estimates Through Belief Propagation.