Introduction to Molecular Biology DNA, RNA, Protein Genome, Chromosome, and Gene Replication and Mutation of DNA Central Dogma (From DNA to Protein) Post-Translation Modification (PTM) Population Genetics Basic Biotechnological Tools Brief History of Bioinformatics Sequence Similarity Introduction Global Alignment Problem Local Alignment Semi-Global Alignment Gap Penalty Scoring Function Suffix Tree Introduction Suffix Tree Simple Applications of Suffix Tree Construction of Suffix Tree Suffix Array FM-Index Approximate Searching Problem Database Search Introduction Smith-Waterman Algorithm FastA BLAST Variations of the BLAST Algorithm Q-Gram Alignment Based on Suffix ARrays (QUASAR) Locality-Sensitive Hashing BWT-SW Are Existing Database Searching Methods Sensitive Enough? Multiple Sequence Alignment Introduction Formal Definition of Multiple Sequence Alignment Problem Dynamic Programming Method Center Star Method Progressive Alignment Method Iterative Method Genome Alignment Introduction Maximum Unique Match (MUM) Mutation Sensitive Alignment Dot Plot for Visualizing the Alignment Phylogeny Reconstruction Introduction Character-Based Phylogeny Reconstruction Algorithm Distance-Based Phylogeny Reconstruction Algorithm Bootstrapping Can Tree Reconstruction Methods Infer the Correct Tree? Phylogeny Comparison Introduction Similarity Measurement Dissimilarity Measurements Consensus Tree Problem Genome Rearrangement Introduction Types of Genome Rearrangements Computational Problems Sorting Unsigned Permutation by Reversals Sorting Signed Permutation by Reversals Motif Finding Introduction Identifying Binding Regions of TFs Motif Model The Motif Finding Problem Scanning for Known Motifs Statistical Approaches Combinatorial Approaches Scoring Function Motif Ensemble Methods Can Motif Finders Discover the Correct Motifs? Motif Finding Utilizing Additional Information RNA Secondary Structure Prediction Introduction Obtaining RNA Secondary Structure Experimentally RNA Structure Prediction Based on Sequence Only Structure Prediction with the Assumption That There Is No Pseudoknot Nussinov Folding Algorithm ZUKER Algorithm Structure Prediction with Pseudoknots Peptide Sequencing Introduction Obtaining the Mass Spectrum of a Peptide Modeling the Mass Spectrum of a Fragmented Peptide De novo Peptide Sequencing Using Dynamic Programming De novoSequencing Using Graph-Based Approach Peptide Sequencing via Database Search Population Genetics Introduction Hardy-Weinberg Equilibrium Linkage Disequilibrium Genotype Phasing Tag SNP Selection Association Study References Index Exercises appear at the end of each chapter. >Suffix Array FM-Index Approximate Searching Problem Database Search Introduction Smith-Waterman Algorithm FastA BLAST Variations of the BLAST Algorithm Q-Gram Alignment Based on Suffix ARrays (QUASAR) Locality-Sensitive Hashing BWT-SW Are Existing Database Searching Methods Sensitive Enough? Multiple Sequence Alignment Introduction Formal Definition of Multiple Sequence Alignment Problem Dynamic Programming Method Center Star Method Progressive Alignment Method Iterative Method Genome Alignment Introduction Maximum Unique Match (MUM) Mutation Sensitive Alignment Dot Plot for Visualizing the Alignment Phylogeny Reconstruction Introduction Character-Based Phylogeny Reconstruction Algorithm Distance-Based Phylogeny Reconstruction Algorithm Bootstrapping Can Tree Reconstruction Methods Infer the Correct Tree? Phylogeny Comparison Introduction Similarity Measurement Dissimilarity Measurements Consensus Tree Problem Genome Rearrangement Introduction Types of Genome Rearrangements Computational Problems Sorting Unsigned Permutation by Reversals Sorting Signed Permutation by Reversals Motif Finding Introduction Identifying Binding Regions of TFs Motif Model The Motif Finding Problem Scanning for Known Motifs Statistical Approaches Combinatorial Approaches Scoring Function Motif Ensemble Methods Can Motif Finders Discover the Correct Motifs? Motif Finding Utilizing Additional Information RNA Secondary Structure Prediction Introduction Obtaining RNA Secondary Structure Experimentally RNA Structure Prediction Based on Sequence Only Structure Prediction with the Assumption That There Is No Pseudoknot Nussinov Folding Algorithm ZUKER Algorithm Structure Prediction with Pseudoknots Peptide Sequencing Introduction Obtaining the Mass Spectrum of a Peptide Modeling the Mass Spectrum of a Fragmented Peptide De novo Peptide Sequencing Using Dynamic Programming De novoSequencing Using Graph-Based Approach Peptide Sequencing via Database Search Population Genetics Introduction Hardy-Weinberg Equilibrium Linkage Disequilibrium Genotype Phasing Tag SNP Selection Association Study References Index Exercises appear at the end of each chapter. P>Introduction Maximum Unique Match (MUM) Mutation Sensitive Alignment Dot Plot for Visualizing the Alignment Phylogeny Reconstruction Introduction Character-Based Phylogeny Reconstruction Algorithm Distance-Based Phylogeny Reconstruction Algorithm Bootstrapping Can Tree Reconstruction Methods Infer the Correct Tree? Phylogeny Comparison Introduction Similarity Measurement Dissimilarity Measurements Consensus Tree Problem Genome Rearrangement Introduction Types of Genome Rearrangements Computational Problems Sorting Unsigned Permutation by Reversals Sorting Signed Permutation by Reversals Motif Finding Introduction Identifying Binding Regions of TFs Motif Model The Motif Finding Problem Scanning for Known Motifs Statistical Approaches Combinatorial Approaches Scoring Function Motif Ensemble Methods Can Motif Finders Discover the Correct Motifs? Motif Finding Utilizing Additional Information RNA Secondary Structure Prediction Introduction Obtaining RNA Secondary Structure Experimentally RNA Structure Prediction Based on Sequence Only Structure Prediction with the Assumption That There Is No Pseudoknot Nussinov Folding Algorithm ZUKER Algorithm Structure Prediction with Pseudoknots Peptide Sequencing Introduction Obtaining the Mass Spectrum of a Peptide Modeling the Mass Spectrum of a Fragmented Peptide De novo Peptide Sequencing Using Dynamic Programming De novoSequencing Using Graph-Based Approach Peptide Sequencing via Database Search Population Genetics Introduction Hardy-Weinberg Equilibrium Linkage Disequilibrium Genotype Phasing Tag SNP Selection Association Study References Index Exercises appear at the end of each chapter. n by Reversals Sorting Signed Permutation by Reversals Motif Finding Introduction Identifying Binding Regions of TFs Motif Model The Motif Finding Problem Scanning for Known Motifs Statistical Approaches Combinatorial Approaches Scoring Function Motif Ensemble Methods Can Motif Finders Discover the Correct Motifs? Motif Finding Utilizing Additional Information RNA Secondary Structure Prediction Introduction Obtaining RNA Secondary Structure Experimentally RNA Structure Prediction Based on Sequence Only Structure Prediction with the Assumption That There Is No Pseudoknot Nussinov Folding Algorithm ZUKER Algorithm Structure Prediction with Pseudoknots Peptide Sequencing Introduction Obtaining the Mass Spectrum of a Peptide Modeling the Mass Spectrum of a Fragmented Peptide De novo Peptide Sequencing Using Dynamic Programming De novoSequencing Using Graph-Based Approach Peptide Sequencing via Database Search Population Genetics Introduction Hardy-Weinberg Equilibrium Linkage Disequilibrium Genotype Phasing Tag SNP Selection Association Study References Index Exercises appear at the end of each chapter. ;lt;P>Nussinov Folding Algorithm ZUKER Algorithm Structure Prediction with Pseudoknots Peptide Sequencing Introduction Obtaining the Mass Spectrum of a Peptide Modeling the Mass Spectrum of a Fragmented Peptide De novo Peptide Sequencing Using Dynamic Programming De novoSequencing Using Graph-Based Approach Peptide Sequencing via Database Search Population Genetics Introduction Hardy-Weinberg Equilibrium Linkage Disequ.