Chapter 10 Comparing Large Sequence Sets
Chapter 11 Assembling Sequences
Chapter 12 analyzing rna sequence and structure
Chapter 13 Using Proteomics Techniques
Chapter 14 Cheminformatics
Chapter 1 Using Biological Databases
Chapter 2 Recognizing Functional Domains
Chapter 3 Finding Similarities and Inferring Homologies
Chapter 4 Finding Genes
Chapter 5 Modeling Structure from Sequence
Chapter 6 Inferring Evolutionary Relationships
Chapter 7 Analyzing Expression Patterns
Chapter 8 Analyzing Molecular Interactions
Chapter 9 Building Biological Databases
Foreword & Preface

Appendix 1 User Fundamentals
Appendix 2 Glossary of Bioinformatics Terms
Appendix 3 Fundamentals of Bioinformatics

./Appendix/Appendix 1 User Fundamentals:
1A IUPAC IUB Single-Letter Codes Within Nucleic Acid and Amino Acid Sequences
1B Common File Formats
1C Unix Survival Guide
1D X Window System Survival Guide
1E Sequence File Format Conversion with Command-Line Readse

./Appendix/Appendix 2 Glossary of Bioinformatics Terms:
2 Glossary of Bioinformatics Terms

./Appendix/Appendix 3 Fundamentals of Bioinformatics:
3A An Introduction to Hidden Markov Models

./Chapter 10 Comparing Large Sequence Sets:
Unit 10.1 Introduction to Comparing Large Sequence Sets
Unit 10.2 PipMaker A World Wide Web Server for Genomic Sequence Alignments
Unit 10.3 Using MUMmer to Identify Similar Regions in Large Sequence Sets
Unit 10.4 MultiPipMaker Comparative Alignment Server for Multiple DNA Sequences
Unit 10.5 Using Galaxy to Perform Large-Scale Interactive Data Analyses
Unit 10.6 Obtaining Comparative Genomic Data with the VISTA Family of Computational Tools

./Chapter 11 Assembling Sequences:
Unit 11.1 Large Scale Sequencing
Unit 11.2 Viewing and Editing Assembled Sequences Using Consed
Unit 11.3 Generating a Genome Assembly with PCAP
Unit 11.4 Assembling Genomic DNA Sequences with PHRAP
Unit 11.5 Using the Velvet de novo Assembler for Short-Read Sequencing Technologies
Unit 11.6 RNA-Seq Read Alignments with PALMapper
Unit 11.7 Aligning Short Sequencing Reads with Bowtie
Unit 11.8 Next Generation Sequence Assembly with AMOS

./Chapter 12 analyzing rna sequence and structure:
Unit 12.1 An Overview of RNA Structure Prediction and Applications to RNA Gene Prediction and RNAi Design
Unit 12.2 RNA Secondary Structure Analysis Using the Vienna RNA Package
Unit 12.3 RNAi Design and Analysis
Unit 12.4 Predicting the Secondary Structure Common to Two RNA Sequences with Dynalign
Unit 12.5 Annotating Non-Coding RNAs with Rfam
Unit 12.6 RNA Secondary Structure Analysis Using RNAstructure
Unit 12.7 Identifying Structural Noncoding RNAs Using RNAz
Unit 12.8 RNA Secondary Structure Analysis Using The RNAshapes Package
Unit 12.9 miRBase: microRNA Sequences and Annotation

./Chapter 13 Using Proteomics Techniques:
Unit 13.10 De Novo Interpretation of Tandem Mass Spectra
Unit 13.11 Extracting Biological Meaning from Large Gene Lists with DAVID
Unit 13.12 Census for Proteome Quantification
Unit 13.13 Analyzing Shotgun Proteomic Data with PatternLab for Proteomics
Unit 13.14 Predicting Peptide Retention Times for Proteomics
Unit 13.1 Proteomics and the Analysis of Proteomic Data An Overview of Current Protein-Profiling Technologies
Unit 13.2 Finding Protein Sequences Using PROWL
Unit 13.3 Protein Identification Using TurboSEQUEST
Unit 13.4 Validation of Tandem Mass Spectrometry Database Search Results Using DTASelect
Unit 13.5 Installation and Use of the Computational Proteomics Analysis System (CPAS)
Unit 13.6 Using ProSight PTM and Related Tools for Targeted Protein Identification and Characterization with High Mass Accuracy Tandem MS Data
Unit 13.7 Using BiblioSpec for Creating and Searching Tandem MS Peptide Libraries
Unit 13.8 Using the Proteomics Identifications Database (PRIDE)
Unit 13.9 Using GFS to Identify Encoding Genomic Loci from Protein Mass Spectral Data

./Chapter 14 Cheminformatics:
Unit 14.10 Metabolomic Data Processing, Analysis, and Interpretation Using MetaboAnalyst
Unit 14.1 Introduction to Cheminformatics
Unit 14.2 Using Pharmabase to Perform Pharmacological Analyses of Cell Function
Unit 14.3 Using MSDchem to Search the PDB Ligand Dictionary
Unit 14.4 In Silico Drug Exploration and Discovery Using DrugBank
Unit 14.5 Using ChemBank to Probe Chemical Biology
Unit 14.6 Using ZINC to Acquire a Virtual Screening Library
Unit 14.7 PharmGKB An Integrated Resource of Pharmacogenomic Data and Knowledge
Unit 14.8 Exploring Human Metabolites Using the Human Metabolome Database
Unit 14.9 ChEBI: An Open Bioinformatics and Cheminformatics Resource

./Chapter 1 Using Biological Databases:
Unit 1.10 Human Mutation Databases
Unit 1.11 Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes
Unit 1.12 Using the KEGG Database Resource
Unit 1.13 The Human Gene Mutation Database (HGMD) and Its Exploitation in the Study of Mutational Mechanisms
Unit 1.14 Exploring Phenotypic Data at the Rat Genome Database
Unit 1.15 Using the Ensembl Genome Server to Browse Genomic Sequence Data
Unit 1.16 Using the iHOP Information Resource to Mine the Biomedical Literature on Genes, Proteins, and Chemical Compounds
Unit 1.17 Using the MetaCyc Pathway Database and the BioCyc Database Collection
Unit 1.18 Exploring ZebraÞsh Genomic, Functional and Phenotypic Data Using ZFIN
Unit 1.19 Searching NCBI’s dbSNP Database
Unit 1.1 The Importance of Biological Databases in Biological Discovery
Unit 1.2 Searching Online Mendelian Inheritance in Man (OMIM) for Information for Genetic Loci Involved in Human Disease
Unit 1.3 Searching NCBI Databases Using Entrez
Unit 1.4 The UCSC Genome Browser
Unit 1.5 Using the NCBI Map Viewer to Browse Genomic Sequence Data
Unit 1.6 Using the TIGR Gene Index Databases for Biological Discovery
Unit 1.7 Searching the Mouse Genome Informatics (MGI) Resources for Information on Mouse Biology from Genotype to Phenotype
Unit 1.8 Searching WormBase for Information about Caenorhabditis elegans
Unit 1.9 Using the Tools and Resources of the RCSB Protein Data Bank

./Chapter 2 Recognizing Functional Domains:
Unit 2.10 Using the Structure-Function Linkage Database to Characterize Functional Domains in Enzymes
Unit 2.11 Using Weeder for the Discovery of Conserved Transcription Factor Binding Sites
Unit 2.12 Using PhyloCon to Identify Conserved Regulatory Motifs
Unit 2.13 Using CisGenome to Analyze ChIP-chip and ChIP-seq Data
Unit 2.14 Using MACS to Identify Peaks from ChIP-Seq Data
Unit 2.1 An Introduction to Recognizing Functional Domains
Unit 2.2 Using the Blocks Database to Recognize Functional Domains
Unit 2.3 Multiple Sequence Alignment Using ClustalW and ClustalX
Unit 2.4 Discovering Novel Sequence Motifs with MEME
Unit 2.5 Identifying Protein Domains with the Pfam Database
Unit 2.6 Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence
Unit 2.7 The InterPro Database and Tools for Protein Domain Analysis
Unit 2.8 Using the Gibbs Motif Sampler to Find Conserved Domains in DNA and Protein Sequences
Unit 2.9 Using CorePromoter to Find Human Core Promoters

./Chapter 3 Finding Similarities and Inferring Homologies:
Unit 3.10 Mathematically Complete Nucleotide and Protein Sequence Searching Using Ssearch
Unit 3.11 Installing, Maintaining, and Using a Local Copy of BLAST for Intranet and Workstation Use
Unit 3.1 An Overview of Sequence Similarity (“Homology”) Searching
Unit 3.2 Finding Homologs to Nucleic Acid or Protein Sequences Using the Framesearch Program
Unit 3.3 Finding Homologs to Nucleotide Sequences Using Network BLAST Searches
Unit 3.4 Finding Homologs in Amino Acid Sequences Using Network BLAST Searches
Unit 3.5 Selecting the Right Protein-Scoring Matrix
Unit 3.6 Constructing and Refining Multiple Sequence Alignments with PileUp, SeqLab, and the GCG Suite
Unit 3.7 An Overview of Multiple Sequence Alignment
Unit 3.8 Computing Multiple Sequence-Structure Alignments with the T-Coffee Package
Unit 3.9 Finding Protein and Nucleotide Similarities with FASTA

./Chapter 4 Finding Genes:
Unit 4.10 Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
Unit 4.1 An Overview of Gene Identification Approaches, Strategies, and Considerations
Unit 4.2 Using MZEF to Find Internal Coding Exons
Unit 4.3 Using geneid to Identify Genes
Unit 4.4 Using GlimmerM to Find Genes in Eukaryotic Genomes
Unit 4.5 Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm
Unit 4.6 Eukaryotic Gene Prediction Using GeneMark.hmm
Unit 4.7 Application of FirstEF to Find Promoters and First Exons in the Human Genome
Unit 4.8 Using N-SCAN or TWINSCAN to Predict Gene Structures in Genomic DNA Sequences
Unit 4.9 GrailEXP and Genome Analysis Pipeline for Genome Annotation

./Chapter 5 Modeling Structure from Sequence:
Unit 5.1 An Introduction to Modeling Structure from Sequence
Unit 5.2 FAMS and FAMSBASE for Protein Structure
Unit 5.3 Modeling Membrane Proteins Utilizing Information from Silent Amino Acid Substitutions
Unit 5.4 Representing Structural Information with RasMol
Unit 5.5 Using Dali for Structural Comparison of Proteins
Unit 5.6 Comparative Protein Structure Modeling Using Modeller
Unit 5.7 Using VMD: An Introductory Tutorial

./Chapter 6 Inferring Evolutionary Relationships:
Unit 6.10 Using OrthoCluster for the Detection of Synteny Blocks Among Multiple Genomes
Unit 6.11 Inferring Protein Function from Homology Using the Princeton Protein Orthology Database (P-POD)
Unit 6.1 Introduction to Inferring Evolutionary Relationships
Unit 6.2 Visualizing Phylogenetic Trees Using TreeView
Unit 6.3 Getting a Tree Fast Neighbor Joining, FastME, and Distance-Based Methods
Unit 6.4 Inferring Evolutionary Trees with PAUP*
Unit 6.5 Using MODELTEST and PAUP* to Select a Model of Nucleotide Substitution
Unit 6.6 Maximum-Likelihood Analysis Using TREE-PUZZLE
Unit 6.7 What If I Don’t Have a Tree Split Decomposition and Related Models
Unit 6.8 Using PEBBLE for the Evolutionary Analysis of Serially Sampled Molecular Sequences
Unit 6.9 Phylogenomic Inference of Protein Molecular Function

./Chapter 7 Analyzing Expression Patterns:
Unit 7.10 Microarray Data Visualization and Analysis with the Longhorn Array Database (LAD)
Unit 7.11 Gene Expression Analysis via Multidimensional Scaling
Unit 7.12 Using GenePattern for Gene Expression Analysis
Unit 7.13 Data Storage and Analysis in ArrayExpress and Expression Profiler
Unit 7.14 Analyzing Gene Expression Data from Microarray and Next-Generation DNA Sequencing Transcriptome Profiling Assays Using GeneSifter Analysis Edition
Unit 7.1 Analysis of Expression Data An Overview
Unit 7.2 The Gene Ontology (GO) Project: Structured Vocabularies for Molecular Biology and Their Application to Genome and Expression Analysis
Unit 7.3 Analysis of Gene-Expression Data Using J-Express
Unit 7.4 DRAGON and DRAGON View Information Annotation and Visualization Tools for Large-Scale Expression Data
Unit 7.5 Using GenMAPP and MAPPFinder to View Microarray Data on Biological Pathways and Identify Global Trends in the Data
Unit 7.6 Integrating Whole-Genome Expression Results into Metabolic Networks with Pathway Processor
Unit 7.7 An Overview of Spotfire for Gene-Expression Studies
Unit 7.8 Loading and Preparing Data for Analysis in Spotfire
Unit 7.9 Analyzing and Visualizing Expression Data with Spotfire

./Chapter 8 Analyzing Molecular Interactions:
Unit 8.10 Active Site Profiling to Identify Protein Functional Sites in Sequences and Structures Using the Deacon Active Site Profiler (DASP)
Unit 8.11 Structure-Based pKa Calculations Using Continuum Electrostatics Methods
Unit 8.12 Flexible Ligand Docking with Glide
Unit 8.13 Exploring Biological Networks with Cytoscape Software
Unit 8.14 Using AutoDock for Ligand-Receptor Docking
Unit 8.1 Analyzing Molecular Interactions
Unit 8.2 Prediction of Protein-Protein Interaction Networks
Unit 8.3 Evaluation of Electrostatic Interactions
Unit 8.4 Using DelPhi to Compute Electrostatic Potentials and Assess Their Contribution to Interactions
Unit 8.5 Searching the MINT Database for Protein Interaction Information
Unit 8.6 Identifying Functional Sites Based on Prediction of Charged Group Behavior
Unit 8.7 Using the Reactome Database
Unit 8.8 Analyzing Networks with VisANT
Unit 8.9 Searching, Viewing, and Visualizing Data in the Biomolecular Interaction Network Database (BIND)

./Chapter 9 Building Biological Databases:
Unit 9.10 Installing a Local Copy of the Reactome Web Site and Database
Unit 9.11 Browsing Multidimensional Molecular Networks with the Generic Network Browser (N-Browse)
Unit 9.12 Using the Generic Synteny Browser (GBrowse syn)
Unit 9.13 Setting Up the JBrowse Genome Browser
Unit 9.14 Administering GBrowse Sites with WebGBrowse
Unit 9.1 Creating Databases for Biological Information An Introduction
Unit 9.2 Structured Query Language (SQL) Fundamentals
Unit 9.3 Modeling Biology Using Relational Databases
Unit 9.4 Using Relational Databases for Improved Sequence Similarity Searching and Large-Scale Genomic Analyses
Unit 9.5 Using Apollo to Browse and Edit Genome Annotations
Unit 9.6 Using Chado to Store Genome Annotation Data
Unit 9.7 PubSearch and PubFetch A Simple Management System for Semiautomated Retrieval and Annotation of Biological Information from the Literature
Unit 9.8 Installing and Configuring CMap
Unit 9.9 Using the Generic Genome Browser (GBrowse)

./Foreword & Preface: