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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

• Extracting Information from Large Multi-Entry Text Files

What Files Can You Access?

Before You Begin

Creating a BioIndexedFile Object to Access Your Source File

Determining the Number of Entries Indexed By a BioIndexedFile Object

Retrieving Entries from Your Source File

Reading Entries from Your Source File

• Storing and Managing Short-Read Sequence Data in Objects

Representing Sequence and Quality Data in a BioRead Object

Representing Sequence, Quality, and Alignment/Mapping Data in a BioMap Object

Retrieving Information from a BioRead or BioMap Object

Setting Information in a BioRead or BioMap Object

Determining Coverage of a Reference Sequence

Constructing Sequence Alignments to a Reference Sequence

Filtering Read Sequences Using SAM Flags

• Storing and Managing Feature Annotations in Objects

Representing Feature Annotations in a GFFAnnotation or GTFAnnotation Object

Constructing an Annotation Object

Retrieving General Information from an Annotation Object

Accessing Data in an Annotation Object

Using Feature Annotations with Short-Read Sequence Data

• Visualizing and Investigating Short-Read Alignments

When to Use the NGS Browser to Visualize and Investigate Data

Opening the NGS Browser

Importing Data into the NGS Browser

Zooming and Panning to a Specific Region of the Alignment

Viewing Coverage of the Reference Sequence

Viewing the Pileup View of Short Reads

Comparing Alignments of Multiple Data Sets

Viewing Location, Quality Scores, and Mapping Information

Evaluating and Flagging Mismatches

Viewing Insertions and Deletions

Viewing Feature Annotations

Printing and Exporting the Browser Image

Identifying Differentially Expressed Genes from RNA-Seq Data

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

• Sequence Analysis

• Microarray Analysis

• Phylogenetic Analysis

• Release Notes

High-Throughput Sequence Analysis

Examples

Extracting Information from Large Multi-Entry Text Files

Extracting Information from Large Multi-Entry Text Files

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