Algorithms in Bioinformatics

An Improved Model for Statistical Alignment.- Improving Profile-Profile Alignments via Log Average Scoring.- False Positives in Genomic Map Assembly and Sequence Validation.- Boosting EM for Radiation Hybrid and Genetic Mapping.- Placing Probes along the Genome Using Pairwise Distance Data.- Comparing a Hidden Markov Model and a Stochastic Context-Free Grammar.- Assessing the Statistical Significance of Overrepresented Oligonucleotides.- Pattern Matching and Pattern Discovery Algorithms for Protein Topologies.- Computing Linking Numbers of a Filtration.- Side Chain-Positioning as an Integer Programming Problem.- A Chemical-Distance-Based Test for Positive Darwinian Selection.- Finding a Maximum Compatible Tree for a Bounded Number of Trees with Bounded Degree Is Solvable in Polynomial Time.- Experiments in Computing Sequences of Reversals.- Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes.- Finding an Optimal Inversion Median: Experimental Results.- Analytic Solutions for Three-Taxon MLMC Trees with Variable Rates Across Sites.- The Performance of Phylogenetic Methods on Trees of Bounded Diameter.- (1+?)-Approximation of Sorting by Reversals and Transpositions.- On the Practical Solution of the Reversal Median Problem.- Algorithms for Finding Gene Clusters.- Determination of Binding Amino Acids Based on Random Peptide Array Screening Data.- A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites.- Comparing Assemblies Using Fragments and Mate-Pairs.

Includes supplementary material: sn.pub/extras