Bioinformatics Toolbox - Documentation

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R2011b Documentation → Bioinformatics Toolbox
View documentation for other releases	Learn more about Bioinformatics Toolbox

Contents

Index

• Getting Started

• Installation

• Features and Functions

Data Formats and Databases

Sequence Alignments

Sequence Utilities and Statistics

Protein Property Analysis

Phylogenetic Analysis

Microarray Data Analysis

Microarray Data Storage

Mass Spectrometry Data Analysis

Graph Theory Functions

Graph Visualization

Statistical Learning and Visualization

Prototyping and Development Environment

Data Visualization

Algorithm Sharing and Application Deployment

• Importing and Exploring Bioinformatic Data from Microsoft Excel

Using Excel and MATLAB Together

About the Example

Before Running the Example

Running the Example for the Entire Data Set

Editing Formulas to Run the Example on a Subset of the Data

Using the Spreadsheet Link EX Interface to Interact With the Data in MATLAB

• Creating get Functions

What Are get Functions?

Creating the getpubmed Function

• Support Vector Machines (SVM)

Understanding Support Vector Machines

Using Support Vector Machines

Example: Nonlinear Classifier with Gaussian Kernel

Example: SVM Classification with Cross Validation

References

• User's Guide

• High-Throughput Sequence Analysis

• Extracting Information from Large Multi-Entry Text Files

• Storing and Managing Short-Read Sequence Data in Objects

• Storing and Managing Feature Annotations in Objects

• Visualizing and Investigating Short-Read Alignments

Identifying Differentially Expressed Genes from RNA-Seq Data

Exploring Protein-DNA Binding Sites from Paired-End ChIP-Seq Data

• Sequence Analysis

• Reading, Analyzing, and Converting a Nucleotide Sequence Using the Command Line

• Importing, Viewing, and Exploring a Nucleotide Sequence Using a Graphical Interface

• Importing, Viewing, and Exploring a Protein Sequence Using a Graphical Interface

• Example: Sequence Alignment

• Viewing and Aligning Multiple Sequences

• Microarray Analysis

Storing and Managing Gene Expression Data in Objects

• Representing Expression Data Values in DataMatrix Objects

• Representing Expression Data Values in ExptData Objects

• Representing Sample and Feature Metadata in MetaData Objects

• Representing Experiment Information in a MIAME Object

• Representing All Data and Information in an ExpressionSet Object

• Example: Visualizing Microarray Images

• Example: Analyzing Gene Expression Profiles

Detecting DNA Copy Number Alteration in Array-Based CGH Data

Exploring Gene Expression Data

• Phylogenetic Analysis

Overview of Phylogenetic Analysis

• Example: Building a Phylogenetic Tree

• Phylogenetic Tree Tool Reference

• Functions

Examples

• Release Notes

	Functions:
	By Category
	Alphabetical List

	Classes:
	Alphabetical List



	Documentation Set

	Getting Started
	Introduction to the features and functions in Bioinformatics Toolbox

	User's Guide
	Procedures for using Bioinformatics Toolbox with MATLAB and Statistics Toolbox

	Examples in Documentation
	Major examples in the Bioinformatics Toolbox documentation



	Product Demos

	Bioinformatics Toolbox Demos
	Presents a collection of demos that help you learn the product



	What's New

	Release Notes
	Summarizes new features, bug fixes, upgrade issues, etc.



	Printable (PDF) Documentation on the Web

	PDF Documents
	Provides printable versions of documentation for Bioinformatics Toolbox

MathWorks Web Site Resources

	Demos
	MATLAB Central
	Product Page
	Platforms & Requirements

	Related Books
	Related Products
	Technical Support

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