Algorithms in Bioinformatics: Second International Workshop, WABI 2002 Rome, Italy, September 17–21, 2002 Proceedings

Simultaneous Relevant Feature Identification and Classification in High-Dimensional Spaces....Pages 1-9
Pooled Genomic Indexing (PGI): Mathematical Analysis and Experiment Design....Pages 10-28
Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem....Pages 29-43
Methods for Inferring Block-Wise Ancestral History from Haploid Sequences....Pages 44-59
Finding Signal Peptides in Human Protein Sequences Using Recurrent Neural Networks....Pages 60-67
Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass Spectrometry....Pages 68-81
Improved Approximation Algorithms for NMR Spectral Peak Assignment....Pages 82-96
Efficient Methods for Inferring Tandem Duplication History....Pages 97-111
Genome Rearrangement Phylogeny Using Weighbor....Pages 112-125
Segment Match Refinement and Applications....Pages 126-139
Extracting Common Motifs under the Levenshtein Measure: Theory and Experimentation....Pages 140-156
Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics....Pages 157-171
FAUST: An Algorithm for Extracting Functionally Relevant Templates from Protein Structures....Pages 172-184
Efficient Unbound Docking of Rigid Molecules....Pages 185-200
A Method of Consolidating and Combining EST and mRNA Alignments to a Genome to Enumerate Supported Splice Variants....Pages 201-209
A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding....Pages 210-219
Comparative Methods for Gene Structure Prediction in Homologous Sequences....Pages 220-234
MultiProt — A Multiple Protein Structural Alignment Algorithm....Pages 235-250
A Hybrid Scoring Function for Protein Multiple Alignment....Pages 251-262
Functional Consequences in Metabolic Pathways from Phylogenetic Profiles....Pages 263-276
Finding Founder Sequences from a Set of Recombinants....Pages 277-286
Estimating the Deviation from a Molecular Clock....Pages 287-299
Exploring the Set of All Minimal Sequences of Reversals — An Application to Test the Replication-Directed Reversal Hypothesis....Pages 300-315
Approximating the Expected Number of Inversions Given the Number of Breakpoints....Pages 316-330
Invited Lecture — Accelerating Smith-Waterman Searches....Pages 331-342
Sequence-Length Requirements for Phylogenetic Methods....Pages 343-356
Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle....Pages 357-374
NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks....Pages 375-391
On the Control of Hybridization Noise in DNA Sequencing-by-Hybridization....Pages 392-403
Restricting SBH Ambiguity via Restriction Enzymes....Pages 404-417
Invited Lecture — Molecule as Computation: Towards an Abstraction of Biomolecular Systems....Pages 418-418
Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search....Pages 419-433
Rapid Large-Scale Oligonucleotide Selection for Microarrays....Pages 434-434
Border Length Minimization in DNA Array Design * ....Pages 435-448
The Enhanced Suffix Array and Its Applications to Genome Analysis....Pages 449-463
The Algorithmic of Gene Teams....Pages 464-476
Combinatorial Use of Short Probes for Differential Gene Expression Profiling....Pages 477-490
Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome....Pages 491-505
 K -ary Clustering with Optimal Leaf Ordering for Gene Expression Data....Pages 506-520
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data....Pages 521-536
Modified Mincut Supertrees....Pages 537-551