Current Protocols in Bioinformatics
Copyright © 1999-2012 by John Wiley and Sons, Inc. All Rights Reserved.
Online ISBN: 9780471250951
DOI: 10.1002/0471250953
Archive
Current Protocols in Bioinformatics Supplements
2013: 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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Supplement 3, September 2003
Unit 1.6 Using the TIGR Gene Index Databases for Biological Discovery
Full Text: HTML PDF
Unit 3.7 An Overview of Multiple Sequence Alignment
Abstract | Full Text: HTML PDF
Unit 4.8 Using TWINSCAN to Predict Gene Structures in Genomic DNA Sequences
Full Text: HTML PDF
Unit 5.1 Modeling Protein Structure from Its Sequence
Full Text: HTML PDF
Unit 7.1 Analysis of Expression Data: An Overview
Full Text: HTML PDF
Supplement 2, June 2003
Unit 2.7 The InterPro Database and Tools for Protein Domain Analysis
Full Text: HTML PDF
Unit 7.4 DRAGON and DRAGON View: Information Annotation and Visualization Tools for Large-Scale Expression Data
Abstract | Full Text: HTML PDF
Unit 8.3 Evaluation of Electrostatic Interactions
Abstract | Full Text: HTML PDF
Unit 8.4 Using DelPhi to Compute Electrostatic Potentials and Assess Their Contribution to Interactions
Abstract | Full Text: HTML PDF
Unit 8.5 Searching the MINT Database for Protein Interaction Information
Full Text: HTML PDF
Unit 11.1 Large Scale Sequencing
Abstract | Full Text: HTML PDF
Unit 11.2 Viewing and Editing Assembled Sequences Using Consed
Abstract | Full Text: HTML PDF
Supplement 1, March 2003
Unit 2.5 Identifying Protein Domains with the Pfam Database
Full Text: HTML PDF
Unit 4.5 Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm
Abstract | Full Text: HTML PDF
Unit 4.6 Eukaryotic Gene Prediction Using GeneMark.hmm
Abstract | Full Text: HTML PDF
Unit 4.7 Application of FirstEF to Find Promoters and First Exons in the Human Genome
Abstract | Full Text: HTML PDF
Unit 6.7 What If I Don't Have a Tree?: Split Decomposition and Related Models
Abstract | Full Text: HTML PDF
Unit 8.1 Analyzing Molecular Interactions
Abstract | Full Text: HTML PDF
Unit 8.2 Prediction of Protein-Protein Interaction Networks
Full Text: HTML PDF
Core Publication, January 2003
Unit 1.1 The Importance of Biological Databases in Biological Discovery
Full Text: HTML PDF
Unit 1.2 Searching Online Mendelian Inheritance in Man (OMIM) for Information for Genetic Loci Involved in Human Disease
Full Text: HTML PDF
Unit 1.3 Searching the NCBI Databases Using Entrez
Full Text: HTML PDF
Unit 1.4 The UCSC Genome Browser
Full Text: HTML PDF
Unit 1.5 Using the NCBI Map Viewer to Browse Genomic Sequence Data
Full Text: HTML PDF
Unit 2.1 An Introduction to Recognizing Functional Domains
Full Text: HTML PDF
Unit 2.2 Using the Blocks Database to Recognize Functional Domains
Abstract | Full Text: HTML PDF
Unit 2.3 Multiple Sequence Alignment Using ClustalW and ClustalX
Abstract | Full Text: HTML PDF
Unit 2.4 Discovering Novel Sequence Motifs with MEME
Abstract | Full Text: HTML PDF
Unit 2.5 Identifying Protein Domains with the Pfam Database
Unit 2.6 Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence
Full Text: HTML PDF
Unit 3.1 An Overview of Sequence Similarity ("Homology") Searching
Full Text: HTML PDF
Unit 3.2 Finding Homologs to Nucleic Acid or Protein Sequences Using the Framesearch Program
Abstract | Full Text: HTML PDF
Unit 3.3 Finding Homologs to Nucleotide Sequences Using Network BLAST Searches
Full Text: HTML PDF
Unit 3.4 Finding Homologs in Amino Acid Sequences Using Network BLAST Searches
Full Text: HTML PDF
Unit 3.5 Selecting the Right Protein-Scoring Matrix
Abstract | Full Text: HTML PDF
Unit 3.6 Constructing and Refining Multiple Sequence Alignments with PileUp, SeqLab, and the GCG Suite
Abstract | Full Text: HTML PDF
Unit 4.1 An Overview of Gene Identification: Approaches, Strategies, and Considerations
Full Text: HTML PDF
Unit 4.2 Using MZEF to Find Internal Coding Exons
Abstract | Full Text: HTML PDF
Unit 4.3 Using geneid to Identify Genes
Full Text: HTML PDF
Unit 4.4 Using GlimmerM to Find Genes in Eukaryotic Genomes
Abstract | Full Text: HTML PDF
Unit 5.1 Modeling Protein Structure from its Sequence
Unit 6.1 Introduction to Inferring Evolutionary Relationships
Abstract | Full Text: HTML PDF
Unit 6.2 Visualizing Phylogenetic Trees Using TreeView
Abstract | Full Text: HTML PDF
Unit 6.3 Getting a Tree Fast: Neighbor Joining and Distance-Based Methods
Full Text: HTML PDF
Unit 6.4 Inferring Evolutionary Trees with PAUP*
Abstract | Full Text: HTML PDF
Unit 6.5 Using MODELTEST and PAUP* to Select a Model of Nucleotide Substitution
Abstract | Full Text: HTML PDF
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
Full Text: HTML PDF
Unit 7.3 Analysis of Gene-Expression Data Using J-Express
Full Text: HTML PDF
Unit 8.1 Analyzing Molecular Interactions
Unit 9.1 Creating Databases for Biological Information: An Introduction
Abstract | Full Text: HTML PDF
Unit 9.2 Structured Query Language (SQL) Fundamentals
Abstract | Full Text: HTML PDF
Unit 9.3 Modeling Biology Using Relational Databases
Abstract | Full Text: HTML PDF
Unit 10.1 Introduction to Comparing Large Sequence Sets
Abstract | Full Text: HTML PDF
Unit 10.2 PipMaker: A World Wide Web Server for Genomic Sequence Alignments
Abstract | Full Text: HTML PDF
Unit 10.3 Using MUMmer to Identify Similar Regions in Large Sequence Sets
Abstract | Full Text: HTML PDF
Appendix 1A IUPAC/IUB Single-Letter Codes Within Nucleic Acid and Amino Acid Sequences
Abstract | Full Text: HTML PDF
Appendix 1B Common File Formats
Appendix 1C Unix Survival Guide
Full Text: HTML PDF
Appendix 1D X Window System Survival Guide
Full Text: HTML PDF
Appendix 1E Sequence File Format Conversion with Command-Line Readseq
Abstract | Full Text: HTML PDF