Current Protocols in Bioinformatics
Table of Contents

Using Biological Databases

1.1 The Importance of Biological Databases in Biological Discovery
1.2 Searching Online Mendelian Inheritance in Man (OMIM) for Information for Genetic Loci Involved in Human Disease
1.3 Searching the NCBI Databases Using Entrez
1.4 The UCSC Genome Browser
1.5 Using the NCBI Map Viewer to Browse Genomic Sequence Data
1.6 Using the TIGR Gene Index Databases for Biological Discovery
1.7 Searching the Mouse Genome Informatics (MGI) Resources for Information on Mouse Biology from Genotype to Phenotype
1.8 Searching WormBase for Information about Caenorhabditis elegans Unit
1.9 Using the Tools and Resources of the RCSB Protein Data Bank 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

Recognizing Functional Domains

2.1 An Introduction to Recognizing Functional Domains
2.2 Using the Blocks Database to Recognize Functional Domains
2.3 Multiple Sequence Alignment Using ClustalW and ClustalX
2.4 Discovering Novel Sequence Motifs with MEME
2.5 Identifying Protein Domains with the Pfam Database
2.6 Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence
2.7 The InterPro Database and Tools for Protein Domain Analysis
2.8 Using the Gibbs Motif Sampler to Find Conserved Domains in DNA and Protein Sequences
2.9 Using CorePromoter to Find Human Core Promoters Unit
2.10 Using the Structure-Function Linkage Database to Characterize Functional Domains in Enzymes 2.11 Using Weeder for the Discovery of Conserved Transcription Factor Binding Sites

Finding Similarities and Inferring Homologies

3.1 An Overview of Sequence Similarity (Homology) Searching
3.2 Finding Homologs to Nucleic Acid or Protein Sequences Using the Framesearch Program
3.3 Finding Homologs to Nucleotide Sequences Using Network BLAST Searches
3.4 Finding Homologs in Amino Acid Sequences Using Network BLAST Searches
3.5 Selecting the Right Protein-Scoring Matrix
3.6 Constructing and Refining Multiple Sequence Alignments with PileUp, SeqLab, and the GCG
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
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

Finding Genes

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

Modeling Structure from Sequence

5.1 Modeling Protein Structure from Its Sequence
5.2 FAMS and FAMSBASE for Protein Structure
5.3 Modeling Membrane Proteins Utilizing Information from Silent Amino Acid Substitutions
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

Inferring Evolutionary Relationships

6.1 Introduction to Inferring Evolutionary Relationships
6.2 Visualizing Phylogenetic Trees Using TreeView
6.3 Getting a Tree Fast: Neighbor Joining and Distance-Based Methods
6.4 Inferring Evolutionary Trees with PAUP*
6.5 Using MODELTEST and PAUP* to Select a Model of Nucleotide Substitution
6.6 Maximum-Likelihood Analysis Using TREE-PUZZLE
6.7 What If I Don't Have a Tree?: Split Decomposition and Related Models
6.8 Using PEBBLE for the Evolutionary Analysis of Serially Sampled Molecular Sequences
6.9 Phylogenomic Inference of Protein Molecular Function

Analyzing Expression Patterns

7.1 Analysis of Expression Data
7.2 The Gene Ontology (GO) Project: Structured Vocabularies for Molecular Biology and Their Application to Genome and Expression Analysis
7.3 Analysis of Gene-Expression Data Using J-Express
7.4 DRAGON and DRAGON View: Information Annotation and Visualization Tools for Large-Scale Expression Data
7.5 Using GenMAPP and MAPPFinder to View Microarray Data on Biological Pathways and Identify Global Trends in the Data
7.6 Integrating Whole-Genome Expression Results into Metabolic Networks with Pathway Processor
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 Unit
7.10 Microarray Data Visualization and Analysis with the Longhorn Array Database (LAD) Unit
7.11 Gene Expression Analysis via Multidimensional Scaling

Analyzing Molecular Interactions

8.1 Analyzing Molecular Interactions
8.2 Prediction of Protein-Protein Interaction Networks
8.3 Evaluation of Electrostatic Interactions
8.4 Using DelPhi to Compute Electrostatic Potentials and Assess Their Contribution to Interactions
8.5 Searching the MINT Database for Protein Interaction Information 
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) Unit
8.10 Active Site Profiling to Identify Protein Functional Sites in Sequences and Structures Using the Deacon Active Site Profiler (DASP)

Building Biological Databases

9.1 Creating Databases for Biological Information: An Introduction
9.2 Structured Query Language (SQL) Fundamentals
9.3 Modeling Biology Using Relational Databases
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

Comparing Large Sequence Sets

10.1 Introduction to Comparing Large Sequence Sets
10.2 PipMaker: A World Wide Web Server for Genomic Sequence Alignments
10.3 Using MUMmer to Identify Similar Regions in Large Sequence Sets
10.4 MultiPipMaker: Comparative Alignment Server for Multiple DNA Sequences

Assembling Sequences
11.1 Large Scale Sequencing
11.2 Viewing and Editing Assembled Sequences Using Consed
11.3 Generating a Genome Assembly with PCAP

Analyzing RNA Sequence and Structure
12.1 An Overview of RNA Structure Prediction
12.2 RNA Secondary Structure Analysis Using the Vienna RNA Package
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

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 Survival Guide
1E Sequence File Format Conversion with Command-Line Readseq

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