Getting Started

   What Is the Bioinformatics Toolbox?
      Expected User

   Installation
      Required Software
      Additional Software

   Features and Functions
      Data Formats and Databases
      Sequence Alignments
      Sequence Utilities and Statistics
      Protein Property Analysis
      Phylogenetic Analysis
      Microarray Data Analysis
      Mass Spectrometry Data Analysis
      Graph Visualization Methods
      Statistical Learning and Visualization
      Prototype and Development Environment
      Data Visualization
      Algorithm Sharing and Application Deployment

Examples

Sequence Analysis

   Example: Sequence Statistics
      Determining Nucleotide Content
      Getting Sequence Information into MATLAB
      Determining Nucleotide Composition
      Determining Codon Composition
      Open Reading Frames
      Amino Acid Conversion and Composition

   Example: Sequence Alignment
      Finding a Model Organism to Study
      Getting Sequence Information from a Public Database
      Searching a Public Database for Related Genes
      Locating Protein Coding Sequences
      Comparing Amino Acid Sequences

Microarray Analysis

   Example: Visualizing Microarray Data
      Overview of the Mouse Example
      Exploring the Microarray Data Set
      Spatial Images of Microarray Data
      Statistics of the Microarrays
      Scatter Plots of Microarray Data

   Example: Analyzing Gene Expression Profiles
      Overview of the Yeast Example
      Exploring the Data Set
      Filtering Genes
      Clustering Genes
      Principal Component Analysis

Phylogenetic Analysis

   Example: Building a Phylogenetic Tree
      Overview for the Primate Example
      Searching NCBI for Phylogenetic Data
      Creating a Phylogenetic Tree for Five Species
      Creating a Phylogenetic Tree for Twelve Species
      Exploring the Phylogenetic Tree

   Phylogenetic Tree Tool Reference
      Opening the Phytreetool GUI
      File Menu
      Tools Menu
      Windows Menu
      Help Menu

Functions – Categorical List

   Data Formats and Databases
   Sequence Conversion
   Sequence Statistics
   Sequence Utilities
   Pairwise Sequence Alignment
   Statistical Learning
   Protein Analysis
   Trace Tools
   Profile Hidden Markov Models
   Microarray File Formats
   Microarray Visualization
   Microarray Normalization and Filtering
   Microarray Utility Functions
   Mass Spectrometry Preprocessing and Visualization
   Scoring Matrices
   Phylogenetic Tree Tools
   Phylogenetic Tree Methods
   Graph Visualization Methods
   Tutorials, Demos, and Examples

Functions — Alphabetical List