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Foreword by Richard J. Roberts, New England Biolabs
Preface
Contributors

CHAPTER 1: USING BIOLOGICAL DATABASES
CHAPTER 2: RECOGNIZING FUNCTIONAL DOMAINS
CHAPTER 3: FINDING SIMILARITIES AND INFERRING HOMOLOGIES
CHAPTER 4: FINDING GENES

CHAPTER 5: MODELING STRUCTURE FROM SEQUENCE
CHAPTER 6: INFERRING EVOLUTIONARY RELATIONSHIPS

CHAPTER 7: ANALYZING EXPRESSION PATTERNS
CHAPTER 8: ANALYZING MOLECULAR INTERACTIONS
CHAPTER 9: BUILDING BIOLOGICAL DATABASES
CHAPTER 10: COMPARING LARGE SEQUENCE SETS
CHAPTER 11: ASSEMBLING SEQUENCES
CHAPTER 12: PROTEIN IDENTIFICATION FROM MASS SPECTROSCOPY
CHAPTER 13: ANALYZING RNA SEQUENCE AND STRUCTURE
APPENDIX 1: USER FUNDAMENTALS
APPENDIX 2: SYSTEM ADMINISTRATOR GUIDELINES

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CHAPTER 1: USING BIOLOGICAL DATABASES, CHAPTER EDITOR - ANDREAS BAXEVANIS

Overview of Biological Databases
Searching Online Mendelian Inheritance in Man (OMIM) for Information on Genetic Loci involved in Human Disease
Searching the NCBI Databases using Entrez
Using the NCBI Map Viewer to Browse Genomic Sequence Data
Using the TIGR Gene Indices for Biological Discovery on New, Gene-Oriented Clusters
Using LocusLink and RefSeq to Access Curated Sequences and Descriptive Information on Genetic
dbSNP: The Database of Single Nucleotide Polymorphisms.
Using UniGene for Biological Discovery on New, Gene-Oriented Clusters
Using the Ensembl Human Genome Server to Browse Genomic Sequence Data
Using the UCSC Human Genome Browser to Browse Genomic Sequence Data
The SRS Information Retrieval System: Using the SRS system to navigate integrated source databases
Saccharomyces Genome Database (SGD)
FlyBase
Kyoto Encyclopedia of Genes and Genomes (KEGG)
CHAPTER 2: RECOGNIZING FUNCTIONAL DOMAINS, CHAPTER EDITOR - GARY STORMO

An Introduction to Recognizing Functional Domains
Using the BLOCKS Database to Recognize Functional Domains
Multiple Sequence Alignment Using CLUSTALW and CLUSTALX
Searching PFAM: A Database of Protein Families
Discovering Novel Sequence Motifs with MEME
The Transcription Element Search System (TESS)
Using the Gibbs Motif Sampler to Find Conserved Domains in DNA and Protein Sequences
Consensus Approach to Identifying Common Motifs in DNA and Protein Sequences
Finding Human Core Promoter Regions
Word-based Pattern Finding Methods
CHAPTER 3: FINDING SIMILARITIES AND INFERRING HOMOLOGIES, CHAPTER EDITOR - DANIEL DAVISON

An Overview of Sequence Similarity (“Homology”) Searching
Finding Homologs to Nucleic Acid or Protein Sequences Using the Framesearch Program
Finding Homologs to Nucleotide Sequences Using Network BLAST Searches
Finding Homologs in Amino Acid Sequences Using Network BLAST Searches
Installing, Maintaining and Using a Local Copy of BLAST
Selecting the Right Scoring Matrices
Finding Similarities Using the Multiple Sequence Alignment Program “PileUp”
Identifying and Using Specialized Protein Scoring Matrices
Finding Nucleotide and Protein Similarities with FASTA
Multiple Sequence Alignment Using T-Coffee
An Overview of Multiple Sequence Alignment Methods
CHAPTER 4: FINDING GENES, CHAPTER EDITOR - ANDREAS BAXEVANIS

An Overview of Gene Identification: Approaches, Strategies, and Considerations
Using MZEF to Find Internal Coding Exons
Using GeneID to Identify Genes
Using GlimmerM to Find Genes in Eukaryotic Organisms
Using RepeatMasker to Detect Repetitive Elements in Nucleotide Sequences
Applying HMMgene for Gene Predictions in Different Organisms
Using GRAIL/GRAIL-EXP to Deduce Gene Structure and Predict New Genes in Newly-Sequenced Regions
Using GeneMark and GeneMark.hmm for Gene Prediction in Prokaryotes
Using GeneMark and GeneMark.hmm for Gene Prediction in Eukaryotes
Annotation of promoters and first exons in the human genome (FirstEF)
Using TWINSCAN to Analyze Eukaryotic Genomic Sequences
CHAPTER 5: MODELING STRUCTURE FROM SEQUENCE, CHAPTER EDITOR - GREGORY PETSKO

An Overview of Modeling Structure from Sequence
Homology Modeling: Methods and Limitations
Modeling Membrane Protein Structures
Use of Database Searches and Simulated Annealing
Generalized Comparative Modeling
Modeling Side-Chain Positions
CHAPTER 6: INFERRING EVOLUTIONARY RELATIONSHIPS, CHAPTER EDITOR - RODERIC PAGE·

Introduction to Inferring Evolutionary Relationships
Visualizing Trees
Getting a Tree Fast: Neighbor-Joining and Distance-based Methods
Inferring Evolutionary Trees with PAUP
Choosing the Best Maximum Likelihood Model for Your Data
Maximum Likelihood Analysis using Tree-Puzzle
Trees with a Timescale What if I Don't Have a Tree?
Bayesian Tree Building
CHAPTER 7: ANALYZING EXPRESSION PATTERNS, CHAPTER EDITOR - ANDREAS BAXEVANIS

Analysis of Expression Data
The Gene Ontology Consortium: A Controlled Vocabulary of Gene Names and its Application to Genomic Discovery
J-Express: A Unified Approach to the Analysis of Gene Expression Data
Gene Microarray Pathway Profiler (GenMAPP): Graphic representation of gene expression values on pathway diagrams
Searching and Submitting to ArrayExpress
DRAGONview: Information Visualization Tools for Microarray Data
CHAPTER 8: ANALYZING MOLECULAR INTERACTIONS, CHAPTER EDITOR - GREGORY PETSKO

An Introduction to Analyzing Molecular Interactions
Prediction of Protein-Protein Interaction Networks
Use of MINT: The Molecular Interactions Database
Evaluation of Electrostatic Interactions
Computation of Electrostatic Potentials and their Contribution to Interactions
CHAPTER 9: BUILDING BIOLOGICAL DATABASES, CHAPTER EDITOR - LINCOLN STEIN

Creating Databases for Biological Information: An Introduction
SQL, Structured Query Language Fundamentals
Relational Modeling of Biological Data
Databasing Gene Ontology Information
Relational Schemas for Biological Pathways
Databasing Sequence Similarity Data
Storing Biological Data with ACeDB
Querying ACeDB
Databasing Sequence Annotation Data
Databasing Microarray Experiments
CHAPTER 10: COMPARING LARGE SEQUENCE SETS, CHAPTER EDITOR - RODERIC PAGE

Introduction to Comparing Large Sequence Sets

PIP MAKER

MUMMER

CHAPTER 11: ASSEMBLING SEQUENCES, CHAPTER EDITOR - LINCOLN STEIN

Coming soon
CHAPTER 12: PROTEIN IDENTIFICATION FROM MASS SPECTROMETRY, CHAPTER EDITOR - DANIEL DAVISON

Coming soon
CHAPTER 13: ANALYZING RNA SEQUENCE AND STRUCTURE, CHAPTER EDITOR - GARY STORMO

Coming soon
APPENDIX 1: USER FUNDAMENTALS

IUPAC Table
Common File Formats
Using UNIX

Using X-Windows
Sequence File Format Conversion
APPENDIX 2: SYSTEM ADMINISTRATOR GUIDELINES

Coming soon

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