Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

Online ISBN: 9780471250951

DOI: 10.1002/0471250953

Archive


 

Current Protocols in Bioinformatics Supplements

2014:    Supplement 48     Supplement 47     Supplement 46     Supplement 45    
2013:    Supplement 44     Supplement 43     Supplement 42     Supplement 41    
2012:    Supplement 40     Supplement 39     Supplement 38     Supplement 37    
2011:    Supplement 36     Supplement 35     Supplement 34     Supplement 33    
2010:    Supplement 32     Supplement 31     Supplement 30     Supplement 29    
2009:    Supplement 28     Supplement 27     Supplement 26     Supplement 25    
2008:    Supplement 24     Supplement 23     Supplement 22     Supplement 21    
2007:    Supplement 20     Supplement 19     Supplement 18     Supplement 17    
2006:    Supplement 16     Supplement 15     Supplement 14     Supplement 13    
2005:    Supplement 12     Supplement 11     Supplement 10     Supplement 9      
2004:    Supplement 8       Supplement 7       Supplement 6       Supplement 5      
2003:    Supplement 4       Supplement 3       Supplement 2       Supplement 1       Core publication




  Supplement 48, December 2014

Unit 1.25 Using the MEROPS Database for Proteolytic Enzymes and Their Inhibitors and Substrates
         Abstract | Full Text:  HTML   PDF

Unit 2.10 Using the Structure-Function Linkage Database to Characterize Functional Domains in Enzymes
         Abstract | Full Text:  HTML   PDF

Unit 3.12 Using EMBL-EBI Services via Web Interface and Programmatically via Web Services
         Abstract | Full Text:  HTML   PDF

Unit 3.13 Clustal Omega
         Abstract | Full Text:  HTML   PDF

Unit 4.11 Genome Annotation and Curation Using MAKER and MAKER-P
         Abstract | Full Text:  HTML   PDF

Unit 8.13 Biological Network Exploration with Cytoscape 3
         Abstract | Full Text:  HTML   PDF

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  Supplement 47, September 2014

Unit 1.24 MalaCards: A Comprehensive Automatically-Mined Database of Human Diseases
         Abstract | Full Text:  HTML   PDF

Unit 2.11 Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences
         Abstract | Full Text:  HTML   PDF

Unit 5.6 Comparative Protein Structure Modeling Using MODELLER
         Abstract | Full Text:  HTML   PDF

Unit 8.13 Biological Network Exploration with Cytoscape 3
         Abstract | Full Text:  HTML   PDF

Unit 11.12 BEDTools: The Swiss-Army Tool for Genome Feature Analysis
         Abstract | Full Text:  HTML   PDF

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  Supplement 46, June 2014

Unit 12.4 Using the RNAstructure Software Package to Predict Conserved RNA Structures
         Abstract | Full Text:  HTML   PDF

Unit 12.6 RNA Secondary Structure Analysis Using RNAstructure
         Abstract | Full Text:  HTML   PDF

Unit 13.24 Employing ProteoWizard to Convert Raw Mass Spectrometry Data
         Abstract | Full Text:  HTML   PDF

Unit 13.25 Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics
         Abstract | Full Text:  HTML   PDF

Unit 13.26 Metaproteomics: Extracting and Mining Proteome Information to Characterize Metabolic Activities in Microbial Communities
         Abstract | Full Text:  HTML   PDF

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  Supplement 45, March 2014

Unit 8.8 Using VisANT to Analyze Networks
         Abstract | Full Text:  HTML   PDF

Unit 15.5 Using SomaticSniper to Detect Somatic Single Nucleotide Variants
         Abstract | Full Text:  HTML   PDF

Unit 15.6 BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping
         Abstract | Full Text:  HTML   PDF

Appendix 1B Common File Formats
         Abstract | Full Text:  HTML   PDF

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  Supplement 44, December 2013

Unit 1.23 mtDNA Variation and Analysis Using Mitomap and Mitomaster
         Abstract | Full Text:  HTML   PDF

Unit 11.11 Using SOAPaligner for Short Reads Alignment
         Abstract | Full Text:  HTML   PDF

Unit 13.22 STRAP PTM: Software Tool for Rapid Annotation and Differential Comparison of Protein Post-Translational Modifications
         Abstract | Full Text:  HTML   PDF

Unit 13.23 PepArML: A Meta-Search Peptide Identification Platform for Tandem Mass Spectra
         Abstract | Full Text:  HTML   PDF

Unit 15.4 Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection
         Abstract | Full Text:  HTML   PDF

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  Supplement 43, October 2013

Unit 3.5 Selecting the Right Similarity-Scoring Matrix
         Abstract | Full Text:  HTML   PDF

Unit 9.15 Cloud Computing with iPlant Atmosphere
         Abstract | Full Text:  HTML   PDF

Unit 11.10 From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
         Abstract | Full Text:  HTML   PDF

Unit 12.1 An Overview of RNA Sequence Analyses: Structure Prediction, ncRNA Gene Identification, and RNAi Design
         Abstract | Full Text:  HTML   PDF

Unit 14.12 LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms
         Abstract | Full Text:  HTML   PDF

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  Supplement 42, June 2013

Unit 1.22 Using the iPlant Collaborative Discovery Environment
         Abstract | Full Text:  HTML   PDF

Unit 3.1 An Introduction to Sequence Similarity (“Homology”) Searching
         Abstract | Full Text:  HTML   PDF

Unit 6.13 Phylogenetic Analysis with the iPlant Discovery Environment
         Abstract | Full Text:  HTML   PDF

Unit 9.1 Creating Databases for Biological Information: An Introduction
         Abstract | Full Text:  HTML   PDF

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  Supplement 41, March 2013

Unit 1.21 Access Guide to Human Proteinpedia
         Abstract | Full Text:  HTML   PDF

Unit 7.6 Pathway-Based Analysis of Microarray and RNAseq Data Using Pathway Processor 2.0
         Abstract | Full Text:  HTML   PDF

Unit 8.17 Using MEMo to Discover Mutual Exclusivity Modules in Cancer
         Abstract | Full Text:  HTML   PDF

Unit 13.21 Proteomics and the Analysis of Proteomic Data: 2013 Overview of Current Protein-Profiling Technologies
         Abstract | Full Text:  HTML   PDF

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  Supplement 40, December 2012

Unit 1.4 The UCSC Genome Browser
         Abstract | Full Text:  HTML   PDF

Unit 1.14 Exploring Genetic, Genomic, and Phenotypic Data at the Rat Genome Database
         Abstract | Full Text:  HTML   PDF

Unit 10.10 Using the Wash U Epigenome Browser to Examine Genome-Wide Sequencing Data
         Abstract | Full Text:  HTML   PDF

Unit 13.19 PatternLab: From Mass Spectra to Label-Free Differential Shotgun Proteomics
         Abstract | Full Text:  HTML   PDF

Unit 13.20 Byonic: Advanced Peptide and Protein Identification Software
         Abstract | Full Text:  HTML   PDF

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  Supplement 39, September 2012

Unit 1.13 The Human Gene Mutation Database (HGMD) and Its Exploitation in the Fields of Personalized Genomics and Molecular Evolution
         Abstract | Full Text:  HTML   PDF

Unit 8.15 Analyzing Protein-Protein Interactions from Affinity Purification-Mass Spectrometry Data with SAINT
         Abstract | Full Text:  HTML   PDF

Unit 8.16 Using ProHits to Store, Annotate, and Analyze Affinity Purification–Mass Spectrometry (AP-MS) Data
         Abstract | Full Text:  HTML   PDF

Unit 12.11 Comparative ncRNA Gene and Structure Prediction Using Foldalign and FoldalignM
         Abstract | Full Text:  HTML   PDF

Unit 15.2 Some Phenotype Association Tools in Galaxy: Looking for Disease SNPs in a Full Genome
         Abstract | Full Text:  HTML   PDF

Unit 15.3 Genotyping in the Cloud with Crossbow
         Abstract | Full Text:  HTML   PDF

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  Supplement 38, June 2012

Unit 1.12 Using the KEGG Database Resource
         Abstract | Full Text:  HTML   PDF

Unit 8.7 Using the Reactome Database
         Abstract | Full Text:  HTML   PDF

Unit 10.5 Using Galaxy to Perform Large-Scale Interactive Data Analyses
         Abstract | Full Text:  HTML   PDF

Unit 11.9 Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy
         Abstract | Full Text:  HTML   PDF

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  Supplement 37, March 2012

Unit 1.2 Searching Online Mendelian Inheritance in Man (OMIM) for Information on Genetic Loci Involved in Human Disease
         Abstract | Full Text:  HTML   PDF

Unit 10.8 Using BLAT to Find Sequence Similarity in Closely Related Genomes
         Abstract | Full Text:  HTML   PDF

Unit 10.9 The Bluejay Genome Browser
         Abstract | Full Text:  HTML   PDF

Unit 13.17 Identifying Proteomic LC-MS/MS Data Sets with Bumbershoot and IDPicker
         Abstract | Full Text:  HTML   PDF

Unit 13.18 Identification of Peptide Features in Precursor Spectra Using Hardklör and Krönik
         Abstract | Full Text:  HTML   PDF

Unit 14.11 LC-MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine
         Abstract | Full Text:  HTML   PDF

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  Supplement 36, December 2011

Unit 8.1 Analyzing Molecular Interactions
         Abstract | Full Text:  HTML   PDF

Unit 10.7 Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities
         Abstract | Full Text:  HTML   PDF

Unit 11.1 An Introduction to the Informatics of “Next-Generation” Sequencing
         Abstract | Full Text:  HTML   PDF

Unit 12.10 Identification of Novel and Known miRNAs in Deep-Sequencing Data with miRDeep2
         Abstract | Full Text:  HTML   PDF

Unit 13.5 Installation and Use of LabKey Server for Proteomics
         Abstract | Full Text:  HTML   PDF

Unit 13.16 Using the scan-x Web Site to Predict Protein Post-Translational Modifications
         Abstract | Full Text:  HTML   PDF

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  Supplement 35, September 2011

Unit 1.20 Using the Saccharomyces Genome Database (SGD) for Analysis of Genomic Information
         Abstract | Full Text:  HTML   PDF

Unit 4.5 Gene Identification in Prokaryotic Genomes, Phages, Metagenomes, and EST Sequences with GeneMarkS Suite
         Abstract | Full Text:  HTML   PDF

Unit 4.6 Eukaryotic Gene Prediction Using GeneMark.hmm-E and GeneMark-ES
         Abstract | Full Text:  HTML   PDF

Unit 6.12 Using OrthoMCL to Assign Proteins to OrthoMCL-DB Groups or to Cluster Proteomes Into New Ortholog Groups
         Abstract | Full Text:  HTML   PDF

Unit 13.15 Biological Sequence Motif Discovery Using motif-x
         Abstract | Full Text:  HTML   PDF

Appendix 2 Glossary of Bioinformatics Terms
         Abstract | Full Text:  HTML   PDF

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  Supplement 34, June 2011

Unit 1.1 The Importance of Biological Databases in Biological Discovery
         Abstract | Full Text:  HTML   PDF

Unit 1.3 Searching NCBI Databases Using Entrez
         Abstract | Full Text:  HTML   PDF

Unit 2.1 An Introduction to Recognizing Functional Domains
         Abstract | Full Text:  HTML   PDF

Unit 2.14 Using MACS to Identify Peaks from ChIP-Seq Data
         Abstract | Full Text:  HTML   PDF

Unit 14.10 Metabolomic Data Processing, Analysis, and Interpretation Using MetaboAnalyst
         Abstract | Full Text:  HTML   PDF

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  Supplement 33, March 2011

Unit 2.13 Using CisGenome to Analyze ChIP-chip and ChIP-seq Data
         Abstract | Full Text:  HTML   PDF

Unit 6.11 Inferring Protein Function from Homology Using the Princeton Protein Orthology Database (P-POD)
         Abstract | Full Text:  HTML   PDF

Unit 9.14 Administering GBrowse Sites with WebGBrowse
         Abstract | Full Text:  HTML   PDF

Unit 11.8 Next Generation Sequence Assembly with AMOS
         Abstract | Full Text:  HTML   PDF

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  Supplement 32, December 2010

Unit 1.19 Searching NCBI’s dbSNP Database
         Abstract | Full Text:  HTML   PDF

Unit 9.13 Setting Up the JBrowse Genome Browser
         Abstract | Full Text:  HTML   PDF

Unit 11.6 RNA-Seq Read Alignments with PALMapper
         Abstract | Full Text:  HTML   PDF

Unit 11.7 Aligning Short Sequencing Reads with Bowtie
         Abstract | Full Text:  HTML   PDF

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  Supplement 31, September 2010

Unit 1.18 Exploring Zebrafish Genomic, Functional and Phenotypic Data Using ZFIN
         Abstract | Full Text:  HTML   PDF

Unit 9.12 Using the Generic Synteny Browser (GBrowse_syn)
         Abstract | Full Text:  HTML   PDF

Unit 11.5 Using the Velvet de novo Assembler for Short-Read Sequencing Technologies
         Abstract | Full Text:  HTML   PDF

Unit 13.14 Predicting Peptide Retention Times for Proteomics
         Abstract | Full Text:  HTML   PDF

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  Supplement 30, June 2010

Unit 1.11 Using The Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes
         Abstract | Full Text:  HTML   PDF

Unit 1.15 Using the Ensembl Genome Server to Browse Genomic Sequence Data
         Abstract | Full Text:  HTML   PDF

Unit 10.4 MultiPipMaker: A Comparative Alignment Server for Multiple DNA Sequences
         Abstract | Full Text:  HTML   PDF

Unit 13.13 Analyzing Shotgun Proteomic Data with PatternLab for Proteomics
         Abstract | Full Text:  HTML   PDF

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  Supplement 29, March 2010

Unit 1.5 Using the NCBI Map Viewer to Browse Genomic Sequence Data
         Abstract | Full Text:  HTML   PDF

Unit 1.6 Using the DFCI Gene Index Databases for Biological Discovery
         Abstract | Full Text:  HTML   PDF

Unit 3.8 Computing Multiple Sequence/Structure Alignments with the T-Coffee Package
         Abstract | Full Text:  HTML   PDF

Unit 12.9 miRBase: microRNA Sequences and Annotation
         Abstract | Full Text:  HTML   PDF

Unit 13.12 Census for Proteome Quantification
         Abstract | Full Text:  HTML   PDF

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  Supplement 28, December 2009

Unit 1.4 The UCSC Genome Browser
         Abstract | Full Text:  HTML   PDF

Unit 9.9 Using the Generic Genome Browser (GBrowse)
         Abstract | Full Text:  HTML   PDF

Unit 13.3 Protein Identification Using Sorcerer 2 and SEQUEST
         Abstract | Full Text:  HTML   PDF

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  Supplement 27, September 2009

Unit 1.1 The Importance of Biological Databases in Biological Discovery
         Abstract | Full Text:  HTML   PDF

Unit 1.2 Searching Online Mendelian Inheritance in Man (OMIM) for Information on Genetic Loci Involved in Human Disease
         Abstract | Full Text:  HTML   PDF

Unit 3.1 An Introduction to Sequence Similarity ("Homology") Searching
         Abstract | Full Text:  HTML   PDF

Unit 6.10 Using OrthoCluster for the Detection of Synteny Blocks Among Multiple Genomes
         Abstract | Full Text:  HTML   PDF

Unit 7.14 Analyzing Gene Expression Data from Microarray and Next-Generation DNA Sequencing Transcriptome Profiling Assays Using GeneSifter Analysis Edition
         Abstract | Full Text:  HTML   PDF

Unit 13.11 Extracting Biological Meaning from Large Gene Lists with DAVID
         Abstract | Full Text:  HTML   PDF

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  Supplement 26, June 2009

Unit 3.3 Finding Similar Nucleotide Sequences Using Network BLAST Searches
         Abstract | Full Text:  HTML   PDF

Unit 10.6 Obtaining Comparative Genomic Data with the VISTA Family of Computational Tools
         Abstract | Full Text:  HTML   PDF

Unit 12.2 RNA Secondary Structure Analysis Using the Vienna RNA Package
         Abstract | Full Text:  HTML   PDF

Unit 12.8 RNA Secondary Structure Analysis Using the RNAshapes Package
         Abstract | Full Text:  HTML   PDF

Unit 14.9 ChEBI: An Open Bioinformatics and Cheminformatics Resource
         Abstract | Full Text:  HTML   PDF

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  Supplement 25, March 2009

Unit 1.7 Searching the Mouse Genome Informatics for Information on Mouse Biology
         Abstract | Full Text:  HTML   PDF

Unit 3.4 Finding Homologs in Amino Acid Sequences Using Network BLAST Searches
         Abstract | Full Text:  HTML   PDF

Unit 4.10 Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
         Abstract | Full Text:  HTML   PDF

Unit 13.10 De Novo Interpretation of Tandem Mass Spectra
         Abstract | Full Text:  HTML   PDF

Unit 14.8 Exploring Human Metabolites Using the Human Metabolome Database
         Abstract | Full Text:  HTML   PDF

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  Supplement 24, December 2008

Unit 1.3 Searching NCBI Databases Using Entrez
         Abstract | Full Text:  HTML   PDF

Unit 5.7 Using VMD: An Introductory Tutorial
         Abstract | Full Text:  HTML   PDF

Unit 8.14 Using AutoDock for Ligand-Receptor Docking
         Abstract | Full Text:  HTML   PDF

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  Supplement 23, September 2008

Unit 2.5 Identifying Protein Domains with the Pfam Database
         Abstract | Full Text:  HTML   PDF

Unit 7.2 The Gene Ontology (GO) Project
         Abstract | Full Text:  HTML   PDF

Unit 7.13 Data Storage and Analysis in ArrayExpress and Expression Profiler
         Abstract | Full Text:  HTML   PDF

Unit 8.13 Exploring Biological Networks with Cytoscape Software
         Abstract | Full Text:  HTML   PDF

Unit 9.11 Browsing Multidimensional Molecular Networks with the Generic Network Browser (N-Browse)
         Abstract | Full Text:  HTML   PDF

Unit 14.7 PharmKGB: An Integrated Resource of Pharmacogenomic Data and Knowledge
         Abstract | Full Text:  HTML   PDF

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  Supplement 22, June 2008

Unit 7.12 Using GenePattern for Gene Expression Analysis
         Abstract | Full Text:  HTML   PDF

Unit 8.2 Prediction of Protein-Protein Interaction Networks
         Abstract | Full Text:  HTML   PDF

Unit 8.5 Searching the MINT Database for Protein Interaction Information
         Abstract | Full Text:  HTML   PDF

Unit 14.5 Using ChemBank to Probe Chemical Biology
         Abstract | Full Text:  HTML   PDF

Unit 14.6 Using ZINC to Acquire a Virtual Screening Library
         Abstract | Full Text:  HTML   PDF

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  Supplement 21, March 2008

Unit 2.6 Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence
         Abstract | Full Text:  HTML   PDF

Unit 2.7 The InterPro Database and Tools for Protein Domain Analysis
         Abstract | Full Text:  HTML   PDF

Unit 7.3 Analysis of Gene-Expression Data Using J-Express
         Abstract | Full Text:  HTML   PDF

Unit 9.10 Installing a Local Copy of the Reactome Web Site and Database
         Abstract | Full Text:  HTML   PDF

Unit 13.8 Using the Proteomics Identifications Database (PRIDE)
         Abstract | Full Text:  HTML   PDF

Unit 13.9 Using GFS to Identify Encoding Genomic Loci from Protein Mass Spectral Data
         Abstract | Full Text:  HTML   PDF

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  Supplement 20, December 2007

Unit 1.9 Using the Tools and Resources of the RCSB Protein Data Bank
         Abstract | Full Text:  HTML   PDF

Unit 1.16 Using the iHOP Information Resource to Mine the Biomedical Literature on Genes, Proteins, and Chemical Compounds
         Abstract | Full Text:  HTML   PDF

Unit 1.17 Using the MetaCyc Pathway Database and the BioCyc Database Collection
         Abstract | Full Text:  HTML   PDF

Unit 4.8 Using N-SCAN or TWINSCAN to Predict Gene Structures in Genomic DNA Sequences
         Abstract | Full Text:  HTML   PDF

Unit 13.7 Using BiblioSpec for Creating and Searching Tandem MS Peptide Libraries
         Abstract | Full Text:  HTML   PDF

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  Supplement 19, September 2007

Unit 2.12 Using PhyloCon to Identify Conserved Regulatory Motifs
         Abstract | Full Text:  HTML   PDF

Unit 10.5 Using Galaxy to Perform Large-Scale Interactive Data Analyses
         Abstract | Full Text:  HTML   PDF

Unit 12.7 Identifying Structural Noncoding RNAs Using RNAz
         Abstract | Full Text:  HTML   PDF

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

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  Supplement 18, June 2007

Unit 4.3 Using geneid to Identify Genes
         Abstract | Full Text:  HTML   PDF

Unit 8.12 Flexible Ligand Docking with Glide
         Abstract | Full Text:  HTML   PDF

Unit 13.5 Installation and Use of the Computational Proteomics Analysis System (CPAS)
         Abstract | Full Text:  HTML   PDF

Unit 14.1 Introduction to Cheminformatics
         Abstract | Full Text:  HTML   PDF

Unit 14.4 In Silico Drug Exploration and Discovery Using DrugBank
         Abstract | Full Text:  HTML   PDF

Appendix 2 Glossary of Bioinformatics Terms
         Abstract | Full Text:  HTML   PDF

Appendix 3A An Introduction to Hidden Markov Models
         Abstract | Full Text:  HTML   PDF

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  Supplement 17, March 2007

Unit 1.4 The UCSC Genome Browser
         Full Text:  HTML   PDF

Unit 6.6 Maximum-Likelihood Analysis Using TREE-PUZZLE
         Abstract | Full Text:  HTML   PDF

Unit 7.1 Analysis of Expression Data: An Overview
         Abstract | Full Text:  HTML   PDF

Unit 9.8 Installing and Configuring CMap
         Abstract | Full Text:  HTML   PDF

Unit 9.9 Using the Generic Genome Browser (GBrowse)
         Full Text:  HTML   PDF

Unit 11.4 Assembling Genomic DNA Sequences with PHRAP
         Abstract | Full Text:  HTML   PDF

Appendix 1D X Window System Survival Guide
         Abstract | Full Text:  HTML   PDF

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  Supplement 16, December 2006

Unit 1.5 Using the NCBI Map Viewer to Browse Genomic Sequence Data
         Full Text:  HTML   PDF

Unit 1.15 Using the Ensembl Genome Server to Browse Genomic Sequence Data
         Full Text:  HTML   PDF

Unit 8.11 Structure-Based p K a Calculations Using Continuum Electrostatics Methods
         Abstract | Full Text:  HTML   PDF

Unit 13.4 Validation of Tandem Mass Spectrometry Database Search Results Using DTASelect
         Abstract | Full Text:  HTML   PDF

Appendix 1B Common File Formats
         Abstract | Full Text:  HTML   PDF

Appendix 1C Unix Survival Guide
         Abstract | Full Text:  HTML   PDF

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  Supplement 15, September 2006

Unit 2.1 An Introduction to Recognizing Functional Domains
         Abstract | Full Text:  HTML   PDF

Unit 2.11 Using Weeder for the Discovery of Conserved Transcription Factor Binding Sites
         Abstract | Full Text:  HTML   PDF

Unit 5.1 An Introduction to Modeling Structure from Sequence
         Abstract | Full Text:  HTML   PDF

Unit 5.6 Comparative Protein Structure Modeling Using Modeller
         Abstract | Full Text:  HTML   PDF

Unit 6.3 Getting a Tree Fast: Neighbor Joining, FastME, and Distance-Based Methods
         Abstract | Full Text:  HTML   PDF

Unit 14.3 Using MSDchem to Search the PDB Ligand Dictionary
         Abstract | Full Text:  HTML   PDF

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  Supplement 14, June 2006

Unit 1.8 Searching WormBase for Information about Caenorhabditis elegans
         Abstract | Full Text:  HTML   PDF

Unit 1.14 Exploring Phenotypic Data at the Rat Genome Database
         Abstract | Full Text:  HTML   PDF

Unit 5.5 Using Dali for Structural Comparison of Proteins
         Abstract | Full Text:  HTML   PDF

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

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  Supplement 13, March 2006

Unit 1.1 The Importance of Biological Databases in Biological Discovery
         Full Text:  HTML   PDF

Unit 1.3 Searching the NCBI Databases Using Entrez
         Full Text:  HTML   PDF

Unit 2.10 Using the Structure-Function Linkage Database to Characterize Functional Domains in Enzymes
         Abstract | Full Text:  HTML   PDF

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

Unit 12.1 An Overview of RNA Structure Prediction and Applications to RNA Gene Prediction and RNAi Design
         Abstract | Full Text:  HTML   PDF

Unit 12.6 RNA Secondary Structure Analysis Using RNAstructure
         Abstract | Full Text:  HTML   PDF

Unit 14.2 Using Pharmabase to Perform Pharmacological Analyses of Cell Function
         Abstract | Full Text:  HTML   PDF

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  Supplement 12, December 2005

Unit 1.13 The Human Gene Mutation Database (HGMD) and Its Exploitation in the Study of Mutational Mechanisms
         Abstract | Full Text:  HTML   PDF

Unit 8.9 Searching, Viewing, and Visualizing Data in the Biomolecular Interaction Network Database (BIND)
         Abstract | Full Text:  HTML   PDF

Unit 9.5 Using Apollo to Browse and Edit Genome Annotations
         Abstract | Full Text:  HTML   PDF

Unit 9.6 Using Chado to Store Genome Annotation Data
         Abstract | Full Text:  HTML   PDF

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  Supplement 11, September 2005

Unit 1.12 Using the KEGG Database Resource
         Abstract | Full Text:  HTML   PDF

Unit 5.4 Representing Structural Information with RasMol
         Abstract | Full Text:  HTML   PDF

Unit 6.9 Phylogenomic Inference of Protein Molecular Function
         Abstract | Full Text:  HTML   PDF

Unit 11.3 Generating a Genome Assembly with PCAP
         Abstract | Full Text:  HTML   PDF

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  Supplement 10, June 2005

Unit 2.8 Using the Gibbs Motif Sampler to Find Conserved Domains in DNA and Protein Sequences
         Abstract | Full Text:  HTML   PDF

Unit 2.9 Using CorePromoter to Find Human Core Promoters
         Abstract | Full Text:  HTML   PDF

Unit 7.11 Gene Expression Analysis via Multidimensional Scaling
         Abstract | Full Text:  HTML   PDF

Unit 13.1 Proteomics and the Analysis of Proteomic Data: An Overview of Current Protein-Profiling Technologies
         Abstract | Full Text:  HTML   PDF

Unit 13.3 Protein Identification Using TurboSEQUEST
         Full Text:  HTML   PDF

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  Supplement 9, March 2005

Unit 1.9 Using the Tools and Resources of the RCSB Protein Data Bank
         Full Text:  HTML   PDF

Unit 1.10 Human Mutation Databases
         Abstract | Full Text:  HTML   PDF

Unit 1.11 Using The Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes
         Full Text:  HTML   PDF

Unit 10.4 MultiPipMaker: Comparative Alignment Server for Multiple DNA Sequences
         Full Text:  HTML   PDF

Unit 12.5 Annotating Non-Coding RNAs with Rfam
         Abstract | Full Text:  HTML   PDF

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  Supplement 8, December 2004

Unit 7.10 Microarray Data Visualization and Analysis with the Longhorn Array Database (LAD)
         Abstract | Full Text:  HTML   PDF

Unit 8.8 Analyzing Networks with VisANT
         Abstract | Full Text:  HTML   PDF

Unit 12.4 Predicting the Secondary Structure Common to Two RNA Sequences with Dynalign
         Abstract | Full Text:  HTML   PDF

Appendix 2 Glossary of Bioinformatics Terms
         Full Text:  HTML   PDF

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  Supplement 7, September 2004

Unit 1.3 Searching the NCBI Databases Using Entrez
         Full Text:  HTML   PDF

Unit 7.9 Analyzing and Visualizing Expression Data with Spotfire
         Abstract | Full Text:  HTML   PDF

Unit 8.7 Using the Reactome Database
         Abstract | Full Text:  HTML   PDF

Unit 9.4 Using Relational Databases for Improved Sequence Similarity Searching and Large-Scale Genomic Analyses
         Abstract | Full Text:  HTML   PDF

Unit 13.2 Finding Protein Sequences Using PROWL
         Abstract | Full Text:  HTML   PDF

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  Supplement 6, June 2004

Unit 1.8 Searching WormBase for Information about Caenorhabditis elegans
         Full Text:  HTML   PDF

Unit 4.1 An Overview of Gene Identification: Approaches, Strategies, and Considerations
         Abstract | Full Text:  HTML   PDF

Unit 7.7 An Overview of Spotfire for Gene-Expression Studies
         Abstract | Full Text:  HTML   PDF

Unit 7.8 Loading and Preparing Data for Analysis in Spotfire
         Abstract | Full Text:  HTML   PDF

Unit 8.6 Identifying Functional Sites Based on Prediction of Charged Group Behavior
         Abstract | Full Text:  HTML   PDF

Unit 12.3 RNAi: Design and Analysis
         Abstract | Full Text:  HTML   PDF

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  Supplement 5, March 2004

Unit 1.7 Searching the Mouse Genome Informatics (MGI) Resources for Information on Mouse Biology from Genotype to Phenotype
        Full Text:  HTML   PDF

Unit 3.11 Installing, Maintaining, and Using a Local Copy of BLAST for Intranet and Workstation Use
         Abstract | Full Text:  HTML   PDF

Unit 4.10 Using Repeat Masker to Identify Repetitive Elements in Genomic Sequences
        Full Text:  HTML   PDF

Unit 6.8 Using PEBBLE for the Evolutionary Analysis of Serially Sampled Molecular Sequences
         Abstract | Full Text:  HTML   PDF

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

Unit 7.6 Integrating Whole-Genome Expression Results into Metabolic Networks with Pathway Processor
         Abstract | Full Text:  HTML   PDF

Appendix 1B Common File Formats
         Full Text:  HTML   PDF

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  Supplement 4, December 2003

Unit 3.8 Computing Multiple Sequence/Structure Alignments with the T-Coffee Package
         Full Text:  HTML   PDF

Unit 3.9 Finding Protein and Nucleotide Similarities with FASTA
         Abstract | Full Text:  HTML   PDF

Unit 3.10 Mathematically Complete Nucleotide and Protein Sequence Searching Using Ssearch
         Abstract | Full Text:  HTML   PDF

Unit 4.9 Grail EXP and Genome Analysis Pipeline for Genome Annotation
         Abstract | Full Text:  HTML   PDF

Unit 5.2 FAMS and FAMSBASE for Protein Structure
         Abstract | Full Text:  HTML   PDF

Unit 5.3 Modeling Membrane Proteins Utilizing Information from Silent Amino Acid Substitutions
         Abstract | Full Text:  HTML   PDF

Unit 12.1 An Overview of RNA Structure Prediction
         Full Text:  HTML   PDF

Unit 12.2 RNA Secondary Structure Analysis Using the Vienna RNA Package
         Full Text:  HTML   PDF

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  Supplement 3, September 2003

Unit 1.6 Using the TIGR Gene Index Databases for Biological Discovery
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Unit 3.7 An Overview of Multiple Sequence Alignment
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Unit 4.8 Using TWINSCAN to Predict Gene Structures in Genomic DNA Sequences
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Unit 5.1 Modeling Protein Structure from Its Sequence
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Unit 7.1 Analysis of Expression Data: An Overview
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  Supplement 2, June 2003

Unit 2.7 The InterPro Database and Tools for Protein Domain Analysis
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Unit 7.4 DRAGON and DRAGON View: Information Annotation and Visualization Tools for Large-Scale Expression Data
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Unit 8.3 Evaluation of Electrostatic Interactions
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Unit 8.4 Using DelPhi to Compute Electrostatic Potentials and Assess Their Contribution to Interactions
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Unit 8.5 Searching the MINT Database for Protein Interaction Information
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Unit 11.1 Large Scale Sequencing
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Unit 11.2 Viewing and Editing Assembled Sequences Using Consed
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  Supplement 1, March 2003

Unit 2.5 Identifying Protein Domains with the Pfam Database
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Unit 4.5 Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm
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Unit 4.6 Eukaryotic Gene Prediction Using GeneMark.hmm
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Unit 4.7 Application of FirstEF to Find Promoters and First Exons in the Human Genome
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Unit 6.7 What If I Don't Have a Tree?: Split Decomposition and Related Models
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Unit 8.1 Analyzing Molecular Interactions
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Unit 8.2 Prediction of Protein-Protein Interaction Networks
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  Core Publication, January 2003

Unit 1.1 The Importance of Biological Databases in Biological Discovery
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Unit 1.2 Searching Online Mendelian Inheritance in Man (OMIM) for Information for Genetic Loci Involved in Human Disease
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Unit 1.3 Searching the NCBI Databases Using Entrez
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Unit 1.4 The UCSC Genome Browser
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Unit 1.5 Using the NCBI Map Viewer to Browse Genomic Sequence Data
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Unit 2.1 An Introduction to Recognizing Functional Domains
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Unit 2.2 Using the Blocks Database to Recognize Functional Domains
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Unit 2.3 Multiple Sequence Alignment Using ClustalW and ClustalX
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Unit 2.4 Discovering Novel Sequence Motifs with MEME
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Unit 2.5 Identifying Protein Domains with the Pfam Database

Unit 2.6 Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence
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Unit 3.1 An Overview of Sequence Similarity ("Homology") Searching
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Unit 3.2 Finding Homologs to Nucleic Acid or Protein Sequences Using the Framesearch Program
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Unit 3.3 Finding Homologs to Nucleotide Sequences Using Network BLAST Searches
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Unit 3.4 Finding Homologs in Amino Acid Sequences Using Network BLAST Searches
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Unit 3.5 Selecting the Right Protein-Scoring Matrix
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Unit 3.6 Constructing and Refining Multiple Sequence Alignments with PileUp, SeqLab, and the GCG Suite
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Unit 4.1 An Overview of Gene Identification: Approaches, Strategies, and Considerations
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Unit 4.2 Using MZEF to Find Internal Coding Exons
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Unit 4.3 Using geneid to Identify Genes
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Unit 4.4 Using GlimmerM to Find Genes in Eukaryotic Genomes
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Unit 5.1 Modeling Protein Structure from its Sequence

Unit 6.1 Introduction to Inferring Evolutionary Relationships
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Unit 6.2 Visualizing Phylogenetic Trees Using TreeView
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Unit 6.3 Getting a Tree Fast: Neighbor Joining and Distance-Based Methods
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Unit 6.4 Inferring Evolutionary Trees with PAUP*
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Unit 6.5 Using MODELTEST and PAUP* to Select a Model of Nucleotide Substitution
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Unit 7.1 Analysis of Expression Data

Unit 7.2 The Gene Ontology (GO) Project: Structured Vocabularies for Molecular Biology and Their Application to Genome and Expression Analysis
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Unit 7.3 Analysis of Gene-Expression Data Using J-Express
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Unit 8.1 Analyzing Molecular Interactions

Unit 9.1 Creating Databases for Biological Information: An Introduction
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Unit 9.2 Structured Query Language (SQL) Fundamentals
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Unit 9.3 Modeling Biology Using Relational Databases
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Unit 10.1 Introduction to Comparing Large Sequence Sets
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Unit 10.2 PipMaker: A World Wide Web Server for Genomic Sequence Alignments
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Unit 10.3 Using MUMmer to Identify Similar Regions in Large Sequence Sets
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Appendix 1A IUPAC/IUB Single-Letter Codes Within Nucleic Acid and Amino Acid Sequences
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Appendix 1B Common File Formats

Appendix 1C Unix Survival Guide
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Appendix 1D X Window System Survival Guide
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Appendix 1E Sequence File Format Conversion with Command-Line Readseq
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