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R2012a Documentation → Bioinformatics Toolbox
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Contents

Index

• Getting Started

Required Software

Optional Software

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

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

What Are get Functions?

Creating the getpubmed Function

Understanding Support Vector Machines

Using Support Vector Machines

Example: Nonlinear Classifier with Gaussian Kernel

Example: SVM Classification with Cross Validation

• User's Guide

• High-Throughput Sequence Analysis

• Sequence Analysis

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

Overview of Example

Searching the Web for Sequence Information

Reading Sequence Information from the Web

Determining Nucleotide Composition

Determining Codon Composition

Open Reading Frames

Amino Acid Conversion and Composition

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

Overview of the Sequence Tool

Importing a Sequence into the Sequence Tool

Viewing Nucleotide Sequence Information

Searching for Words

Exploring Open Reading Frames

Closing the Sequence Tool

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

Overview of the Sequence Tool

Viewing Amino Acid Sequence Statistics

Closing the Sequence Tool

• Example: Sequence Alignment

Overview of Example

Finding a Model Organism to Study

Retrieving Sequence Information from a Public Database

Searching a Public Database for Related Genes

Locating Protein Coding Sequences

Comparing Amino Acid Sequences

• Viewing and Aligning Multiple Sequences

Overview of the Multiple Sequence Alignment Viewer

Loading Sequence Data and Viewing the Phylogenetic Tree

Selecting a Subset of Data from the Phylogenetic Tree

Aligning Multiple Sequences

Adjusting Multiple Sequence Alignments Manually

Closing the Multiple Sequence Alignment Viewer

• Microarray Analysis

• Phylogenetic Analysis

• Release Notes

Sequence Analysis

Sequence analysis is the process you use to find information about a nucleotide or amino acid sequence using computational methods. Common tasks in sequence analysis are identifying genes, determining the similarity of two genes, determining the protein coded by a gene, and determining the function of a gene by finding a similar gene in another organism with a known function.

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

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

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

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

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