Current Protocols in Bioinformatics

With Current Protocols in Bioinformatics , it's easier than ever for the life scientist to become "fluent" in bioinformatics and master the exciting new frontiers opened up by DNA sequencing.

Updated every three months in all formats, CPBI is constantly evolving to keep pace with the very latest discoveries and developments. A year of these quarterly updates is included in the initial CPBI purchase price. That's 590 pages of new (80%) and revised (20%) content on average every year since the initial publication of the work in April 2002! Presently two volumes in its looseleaf print version, CPBI...

* features step-by-step instructions for working with hundreds of applications and databases from research groups around the globe.
* is designed for research biologists, not computational experts.
* shows how to select the right software parameters, analyze data, interpret results, generate hypotheses, and advance research to new levels.
* includes a valuable appendix on user fundamentals and a glossary of bioinformatics terms.

Edited by: Andreas D. Baxevanis, Editor-in-Chief (Bethesda, Maryland); Gregory A. Petsko (Brandeis University); Lincoln D. Stein (Cold Spring Harbor Laboratory); Gary D. Stormo (Washington University); Guest Editor: John R. Yates III (The Scripps Research Institute); Advisory Editor: Daniel B. Davison (Morrisville, Pennsylvania); Past Editor: Roderic D.M. Page (University of Glasgow)

# Chapter 1 Using Biological Databases

* Unit 1.1 The Importance of Biological Databases in Biological Discovery
Abstract | Full Text: HTML PDF (140K)
* Unit 1.2 Searching Online Mendelian Inheritance in Man (OMIM) for Information for Genetic Loci Involved in Human Disease
Abstract | Full Text: HTML PDF (752K)
* Unit 1.3 Searching NCBI Databases Using Entrez
Abstract | Full Text: HTML PDF (1821K)
* Unit 1.4 The UCSC Genome Browser
Abstract | Full Text: HTML PDF (1323K)
* Unit 1.5 Using the NCBI Map Viewer to Browse Genomic Sequence Data
Abstract | Full Text: HTML PDF (2289K)
* Unit 1.6 Using the TIGR Gene Index Databases for Biological Discovery
Abstract | Full Text: HTML PDF (1248K)
* Unit 1.7 Searching the Mouse Genome Informatics (MGI) Resources for Information on Mouse Biology from Genotype to Phenotype
Abstract | Full Text: HTML PDF (554K)
* Unit 1.8 Searching WormBase for Information about Caenorhabditis elegans
Abstract | Full Text: HTML PDF (3541K)
* Unit 1.9 Using the Tools and Resources of the RCSB Protein Data Bank
Abstract | Full Text: HTML PDF (1719K)
* Unit 1.10 Human Mutation Databases
Abstract | Full Text: HTML PDF (742K)
* Unit 1.11 Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes
Abstract | Full Text: HTML PDF (1818K)
* Unit 1.12 Using the KEGG Database Resource
Abstract | Full Text: HTML PDF (6760K)
* Unit 1.13 The Human Gene Mutation Database (HGMD) and Its Exploitation in the Study of Mutational Mechanisms
Abstract | Full Text: HTML PDF (1197K)
* Unit 1.14 Exploring Phenotypic Data at the Rat Genome Database
Abstract | Full Text: HTML PDF (2363K)
* Unit 1.15 Using the Ensembl Genome Server to Browse Genomic Sequence Data
Abstract | Full Text: HTML PDF (2050K)
* Unit 1.16 Using the iHOP Information Resource to Mine the Biomedical Literature on Genes, Proteins, and Chemical Compounds
Abstract | Full Text: HTML PDF (2373K)
* Unit 1.17 Using the MetaCyc Pathway Database and the BioCyc Database Collection
Abstract | Full Text: HTML PDF (5267K)

# Chapter 2 Recognizing Functional Domains

* Unit 2.1 An Introduction to Recognizing Functional Domains
Abstract | Full Text: HTML PDF (67K)
* Unit 2.2 Using the Blocks Database to Recognize Functional Domains
Abstract | Full Text: HTML PDF (1897K)
* Unit 2.3 Multiple Sequence Alignment Using ClustalW and ClustalX
Abstract | Full Text: HTML PDF (908K)
* Unit 2.4 Discovering Novel Sequence Motifs with MEME
Abstract | Full Text: HTML PDF (2208K)
* Unit 2.5 Identifying Protein Domains with the Pfam Database
Abstract | Full Text: HTML PDF (546K)
* Unit 2.6 Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence
Abstract | Full Text: HTML PDF (1296K)
* Unit 2.7 The InterPro Database and Tools for Protein Domain Analysis
Abstract | Full Text: HTML PDF (1189K)
* Unit 2.8 Using the Gibbs Motif Sampler to Find Conserved Domains in DNA and Protein Sequences
Abstract | Full Text: HTML PDF (1331K)
* Unit 2.9 Using CorePromoter to Find Human Core Promoters
Abstract | Full Text: HTML PDF (301K)
* Unit 2.10 Using the Structure-Function Linkage Database to Characterize Functional Domains in Enzymes
Abstract | Full Text: HTML PDF (1890K)
* Unit 2.11 Using Weeder for the Discovery of Conserved Transcription Factor Binding Sites
Abstract | Full Text: HTML PDF (525K)
* Unit 2.12 Using PhyloCon to Identify Conserved Regulatory Motifs
Abstract | Full Text: HTML PDF (2915K)

# Chapter 3 Finding Similarities and Inferring Homologies

* Unit 3.1 An Overview of Sequence Similarity (“Homology”) Searching
Abstract | Full Text: HTML PDF (109K)
* Unit 3.2 Finding Homologs to Nucleic Acid or Protein Sequences Using the Framesearch Program
Abstract | Full Text: HTML PDF (246K)
* Unit 3.3 Finding Homologs to Nucleotide Sequences Using Network BLAST Searches
Abstract | Full Text: HTML PDF (957K)
* Unit 3.4 Finding Homologs in Amino Acid Sequences Using Network BLAST Searches
Abstract | Full Text: HTML PDF (3143K)
* Unit 3.5 Selecting the Right Protein-Scoring Matrix
Abstract | Full Text: HTML PDF (118K)
* Unit 3.6 Constructing and Refining Multiple Sequence Alignments with PileUp, SeqLab, and the GCG Suite
Abstract | Full Text: HTML PDF (1985K)
* Unit 3.7 An Overview of Multiple Sequence Alignment
Abstract | Full Text: HTML PDF (322K)
* Unit 3.8 Computing Multiple Sequence/Structure Alignments with the T-Coffee Package
Abstract | Full Text: HTML PDF (657K)
* Unit 3.9 Finding Protein and Nucleotide Similarities with FASTA
Abstract | Full Text: HTML PDF (404K)
* Unit 3.10 Mathematically Complete Nucleotide and Protein Sequence Searching Using Ssearch
Abstract | Full Text: HTML PDF (321K)
* Unit 3.11 Installing, Maintaining, and Using a Local Copy of BLAST for Intranet and Workstation Use
Abstract | Full Text: HTML PDF (251K)

# Chapter 4 Finding Genes

* Unit 4.1 An Overview of Gene Identification: Approaches, Strategies, and Considerations
Abstract | Full Text: HTML PDF (274K)
* Unit 4.2 Using MZEF to Find Internal Coding Exons
Abstract | Full Text: HTML PDF (1515K)
* Unit 4.3 Using geneid to Identify Genes
Abstract | Full Text: HTML PDF (1089K)
* Unit 4.4 Using GlimmerM to Find Genes in Eukaryotic Genomes
Abstract | Full Text: HTML PDF (615K)
* Unit 4.5 Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm
Abstract | Full Text: HTML PDF (646K)
* Unit 4.6 Eukaryotic Gene Prediction Using GeneMark.hmm
Abstract | Full Text: HTML PDF (399K)
* Unit 4.7 Application of FirstEF to Find Promoters and First Exons in the Human Genome
Abstract | Full Text: HTML PDF (325K)
* Unit 4.8 Using N-SCAN or TWINSCAN to Predict Gene Structures in Genomic DNA Sequences
Abstract | Full Text: HTML PDF (592K)
* Unit 4.9 GrailEXP and Genome Analysis Pipeline for Genome Annotation
Abstract | Full Text: HTML PDF (543K)
* Unit 4.10 Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
Abstract | Full Text: HTML PDF (488K)

# Chapter 5 Modeling Structure from Sequence

* Unit 5.1 An Introduction to Modeling Structure from Sequence
Abstract | Full Text: HTML PDF (40K)
* Unit 5.2 FAMS and FAMSBASE for Protein Structure
Abstract | Full Text: HTML PDF (730K)
* Unit 5.3 Modeling Membrane Proteins Utilizing Information from Silent Amino Acid Substitutions
Abstract | Full Text: HTML PDF (303K)
* Unit 5.4 Representing Structural Information with RasMol
Abstract | Full Text: HTML PDF (1672K)
* Unit 5.5 Using Dali for Structural Comparison of Proteins
Abstract | Full Text: HTML PDF (1616K)
* Unit 5.6 Comparative Protein Structure Modeling Using Modeller
Abstract | Full Text: HTML PDF (656K)
* Unit 5.7 Using VMD: An Introductory Tutorial
Abstract | Full Text: HTML PDF (1313K)

# Chapter 6 Inferring Evolutionary Relationships

* Unit 6.1 Introduction to Inferring Evolutionary Relationships
Abstract | Full Text: HTML PDF (142K)
* Unit 6.2 Visualizing Phylogenetic Trees Using TreeView
Abstract | Full Text: HTML PDF (266K)
* Unit 6.3 Getting a Tree Fast: Neighbor Joining, FastME, and Distance-Based Methods
Abstract | Full Text: HTML PDF (1224K)
* Unit 6.4 Inferring Evolutionary Trees with PAUP*
Abstract | Full Text: HTML PDF (989K)
* Unit 6.5 Using MODELTEST and PAUP* to Select a Model of Nucleotide Substitution
Abstract | Full Text: HTML PDF (439K)
* Unit 6.6 Maximum-Likelihood Analysis Using TREE-PUZZLE
Abstract | Full Text: HTML PDF (728K)
* Unit 6.7 What If I Don't Have a Tree?: Split Decomposition and Related Models
Abstract | Full Text: HTML PDF (310K)
* Unit 6.8 Using PEBBLE for the Evolutionary Analysis of Serially Sampled Molecular Sequences
Abstract | Full Text: HTML PDF (492K)
* Unit 6.9 Phylogenomic Inference of Protein Molecular Function
Abstract | Full Text: HTML PDF (1094K)

# Chapter 7 Analyzing Expression Patterns

* Unit 7.1 Analysis of Expression Data: An Overview
Abstract | Full Text: HTML PDF (113K)
* Unit 7.2 The Gene Ontology (GO) Project: Structured Vocabularies for Molecular Biology and Their Application to Genome and Expression Analysis
Abstract | Full Text: HTML PDF (205K)
* Unit 7.3 Analysis of Gene-Expression Data Using J-Express
Abstract | Full Text: HTML PDF (2638K)
* Unit 7.4 DRAGON and DRAGON View: Information Annotation and Visualization Tools for Large-Scale Expression Data
Abstract | Full Text: HTML PDF (665K)
* Unit 7.5 Using GenMAPP and MAPPFinder to View Microarray Data on Biological Pathways and Identify Global Trends in the Data
Abstract | Full Text: HTML PDF (656K)
* Unit 7.6 Integrating Whole-Genome Expression Results into Metabolic Networks with Pathway Processor
Abstract | Full Text: HTML PDF (703K)
* Unit 7.7 An Overview of Spotfire for Gene-Expression Studies
Abstract | Full Text: HTML PDF (1383K)
* Unit 7.8 Loading and Preparing Data for Analysis in Spotfire
Abstract | Full Text: HTML PDF (1349K)
* Unit 7.9 Analyzing and Visualizing Expression Data with Spotfire
Abstract | Full Text: HTML PDF (1478K)
* Unit 7.10 Microarray Data Visualization and Analysis with the Longhorn Array Database (LAD)
Abstract | Full Text: HTML PDF (2430K)
* Unit 7.11 Gene Expression Analysis via Multidimensional Scaling
Abstract | Full Text: HTML PDF (297K)
* Unit 7.12 Using GenePattern for Gene Expression Analysis
Abstract | Full Text: HTML PDF (1149K)
* Unit 7.13 Data Storage and Analysis in ArrayExpress and Expression Profiler
Abstract | Full Text: HTML PDF (985K)

# Chapter 8 Analyzing Molecular Interactions

* Unit 8.1 Analyzing Molecular Interactions
Abstract | Full Text: HTML PDF (148K)
* Unit 8.2 Prediction of Protein-Protein Interaction Networks
Abstract | Full Text: HTML PDF (283K)
* Unit 8.3 Evaluation of Electrostatic Interactions
Abstract | Full Text: HTML PDF (344K)
* Unit 8.4 Using DelPhi to Compute Electrostatic Potentials and Assess Their Contribution to Interactions
Abstract | Full Text: HTML PDF (659K)
* Unit 8.5 Searching the MINT Database for Protein Interaction Information
Abstract | Full Text: HTML PDF (556K)
* Unit 8.6 Identifying Functional Sites Based on Prediction of Charged Group Behavior
Abstract | Full Text: HTML PDF (103K)
* Unit 8.7 Using the Reactome Database
Abstract | Full Text: HTML PDF (799K)
* Unit 8.8 Analyzing Networks with VisANT
Abstract | Full Text: HTML PDF (1427K)
* Unit 8.9 Searching, Viewing, and Visualizing Data in the Biomolecular Interaction Network Database (BIND)
Abstract | Full Text: HTML PDF (1689K)
* Unit 8.10 Active Site Profiling to Identify Protein Functional Sites in Sequences and Structures Using the Deacon Active Site Profiler (DASP)
Abstract | Full Text: HTML PDF (800K)
* Unit 8.11 Structure-Based pKa Calculations Using Continuum Electrostatics Methods
Abstract | Full Text: HTML PDF (260K)
* Unit 8.12 Flexible Ligand Docking with Glide
Abstract | Full Text: HTML PDF (2359K)
* Unit 8.13 Exploring Biological Networks with Cytoscape Software
Abstract | Full Text: HTML PDF (640K)
* Unit 8.14 Using AutoDock for Ligand-Receptor Docking
Abstract | Full Text: HTML PDF (1450K)

# Chapter 9 Building Biological Databases

* Unit 9.1 Creating Databases for Biological Information: An Introduction
Abstract | Full Text: HTML PDF (760K)
* Unit 9.2 Structured Query Language (SQL) Fundamentals
Abstract | Full Text: HTML PDF (1955K)
* Unit 9.3 Modeling Biology Using Relational Databases
Abstract | Full Text: HTML PDF (219K)
* Unit 9.4 Using Relational Databases for Improved Sequence Similarity Searching and Large-Scale Genomic Analyses
Abstract | Full Text: HTML PDF (346K)
* Unit 9.5 Using Apollo to Browse and Edit Genome Annotations
Abstract | Full Text: HTML PDF (1223K)
* Unit 9.6 Using Chado to Store Genome Annotation Data
Abstract | Full Text: HTML PDF (1004K)
* Unit 9.7 PubSearch and PubFetch: A Simple Management System for Semiautomated Retrieval and Annotation of Biological Information from the Literature
Abstract | Full Text: HTML PDF (1216K)
* Unit 9.8 Installing and Configuring CMap
Abstract | Full Text: HTML PDF (2106K)
* Unit 9.9 Using the Generic Genome Browser (GBrowse)
Abstract | Full Text: HTML PDF (1172K)
* Unit 9.10 Installing a Local Copy of the Reactome Web Site and Database
Abstract | Full Text: HTML PDF (367K)
* Unit 9.11 Browsing Multidimensional Molecular Networks with the Generic Network Browser (N-Browse)
Abstract | Full Text: HTML PDF (418K)

# Chapter 10 Comparing Large Sequence Sets

* Unit 10.1 Introduction to Comparing Large Sequence Sets
Abstract | Full Text: HTML PDF (44K)
* Unit 10.2 PipMaker: A World Wide Web Server for Genomic Sequence Alignments
Abstract | Full Text: HTML PDF (354K)
* Unit 10.3 Using MUMmer to Identify Similar Regions in Large Sequence Sets
Abstract | Full Text: HTML PDF (189K)
* Unit 10.4 MultiPipMaker: Comparative Alignment Server for Multiple DNA Sequences
Abstract | Full Text: HTML PDF (218K)
* Unit 10.5 Using Galaxy to Perform Large-Scale Interactive Data Analyses
Abstract | Full Text: HTML PDF (1784K)

# Chapter 11 Assembling Sequences

* Unit 11.1 Large Scale Sequencing
Abstract | Full Text: HTML PDF (62K)
* Unit 11.2 Viewing and Editing Assembled Sequences Using Consed
Abstract | Full Text: HTML PDF (719K)
* Unit 11.3 Generating a Genome Assembly with PCAP
Abstract | Full Text: HTML PDF (357K)
* Unit 11.4 Assembling Genomic DNA Sequences with PHRAP
Abstract | Full Text: HTML PDF (317K)

# 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
Abstract | Full Text: HTML PDF (37K)
* Unit 12.2 RNA Secondary Structure Analysis Using the Vienna RNA Package
Abstract | Full Text: HTML PDF (162K)
* Unit 12.3 RNAi: Design and Analysis
Abstract | Full Text: HTML PDF (92K)
* Unit 12.4 Predicting the Secondary Structure Common to Two RNA Sequences with Dynalign
Abstract | Full Text: HTML PDF (213K)
* Unit 12.5 Annotating Non-Coding RNAs with Rfam
Abstract | Full Text: HTML PDF (390K)
* Unit 12.6 RNA Secondary Structure Analysis Using RNAstructure
Abstract | Full Text: HTML PDF (588K)
* Unit 12.7 Identifying Structural Noncoding RNAs Using RNAz
Abstract | Full Text: HTML PDF (870K)

# Chapter 13 Using Proteomics Techniques

* Unit 13.1 Proteomics and the Analysis of Proteomic Data: An Overview of Current Protein-Profiling Technologies
Abstract | Full Text: HTML PDF (249K)
* Unit 13.2 Finding Protein Sequences Using PROWL
Abstract | Full Text: HTML PDF (773K)
* Unit 13.3 Protein Identification Using TurboSEQUEST
Abstract | Full Text: HTML PDF (866K)
* Unit 13.4 Validation of Tandem Mass Spectrometry Database Search Results Using DTASelect
Abstract | Full Text: HTML PDF (917K)
* Unit 13.5 Installation and Use of the Computational Proteomics Analysis System (CPAS)
Abstract | Full Text: HTML PDF (2949K)
* Unit 13.6 Using ProSight PTM and Related Tools for Targeted Protein Identification and Characterization with High Mass Accuracy Tandem MS Data
Abstract | Full Text: HTML PDF (1081K)
* Unit 13.7 Using BiblioSpec for Creating and Searching Tandem MS Peptide Libraries
Abstract | Full Text: HTML PDF (1101K)
* Unit 13.8 Using the Proteomics Identifications Database (PRIDE)
Abstract | Full Text: HTML PDF (1532K)
* Unit 13.9 Using GFS to Identify Encoding Genomic Loci from Protein Mass Spectral Data
Abstract | Full Text: HTML PDF (1669K)

# Chapter 14 Cheminformatics

* Unit 14.1 Introduction to Cheminformatics
Abstract | Full Text: HTML PDF (97K)
* Unit 14.2 Using Pharmabase to Perform Pharmacological Analyses of Cell Function
Abstract | Full Text: HTML PDF (986K)
* Unit 14.3 Using MSDchem to Search the PDB Ligand Dictionary
Abstract | Full Text: HTML PDF (1850K)
* Unit 14.4 In Silico Drug Exploration and Discovery Using DrugBank
Abstract | Full Text: HTML PDF (3624K)
* Unit 14.5 Using ChemBank to Probe Chemical Biology
Abstract | Full Text: HTML PDF (635K)
* Unit 14.6 Using ZINC to Acquire a Virtual Screening Library
Abstract | Full Text: HTML PDF (2220K)
* Unit 14.7 PharmGKB: An Integrated Resource of Pharmacogenomic Data and Knowledge
Abstract | Full Text: HTML PDF (594K)

# Appendix 1 User Fundamentals

* 1A IUPAC/IUB Single-Letter Codes Within Nucleic Acid and Amino Acid Sequences
Abstract | Full Text: HTML PDF (50K)
* 1B Common File Formats
Abstract | Full Text: HTML PDF (282K)
* 1C Unix Survival Guide
Abstract | Full Text: HTML PDF (862K)
* 1D X Window System Survival Guide
Abstract | Full Text: HTML PDF (274K)
* 1E Sequence File Format Conversion with Command-Line Readseq
Abstract | Full Text: HTML PDF (76K)

# Appendix 2 Glossary of Bioinformatics Terms

* 2 Glossary of Bioinformatics Terms
Abstract | Full Text: HTML PDF (87K)

# Appendix 3 Fundamentals of Bioinformatics