MATLAB Bioinformatics ToolboxTM User's Guide

Read, analyze, and visualize genomic and proteomic data. Bioinformatics Toolbox provides algorithms and apps for Next Generation Sequencing (NGS), microarray analysis, mass spectrometry, and gene ontology. Using toolbox functions, you can read genomic and proteomic data from standard file formats such as SAM, FASTA, CEL, and CDF, as well as from online databases such as the NCBI Gene Expression Omnibus and GenBank®. You can explore and visualize this data with sequence browsers, spatial heatmaps, and clustergrams. The toolbox also provides statistical techniques for detecting peaks, imputing values for missing data, and selecting features. You can combine toolbox functions to support common bioinformatics workflows. You can use ChIP-Seq data to identify transcription factors; analyze RNA-Seq data to identify differentially expressed genes; identify copy number variants and SNPs in microarray data; and classify protein profiles using mass spectrometry data. Getting Started Bioinformatics Toolbox Product Description Key Features Product Overview Features Expected Users Data Formats and Databases Sequence Alignments Sequence Utilities and Statistics Protein Property Analysis Phylogenetic Analysis Microarray Data Analysis Tools Microarray Data Storage Mass Spectrometry Data Analysis Graph Theory Functions Graph Visualization Statistical Learning and Visualization Prototyping and Development Environment Data Visualization Exchange Bioinformatics Data Between Excel and MATLAB 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 product to Interact With the Data in MATLAB Get Information from Web Database What Are get Functions? Creating the getpubmed Function High-Throughput Sequence Analysis Work with Next-Generation Sequencing Data Overview What Files Can You Access? Before You Begin Create a BioIndexedFile Object to Access Your Source File Determine the Number of Entries Indexed By a BioIndexedFile Object Retrieve Entries from Your Source File Read Entries from Your Source File Manage Sequence Read Data in Objects Overview Represent Sequence and Quality Data in a BioRead Object Represent Sequence, Quality, and Alignment/Mapping Data in a BioMap Object Retrieve Information from a BioRead or BioMap Object Set Information in a BioRead or BioMap Object Determine Coverage of a Reference Sequence Construct Sequence Alignments to a Reference Sequence Filter Read Sequences Using SAM Flags Store and Manage Feature Annotations in Objects Represent Feature Annotations in a GFFAnnotation or GTFAnnotation Object Construct an Annotation Object Retrieve General Information from an Annotation Object Access Data in an Annotation Object Use Feature Annotations with Sequence Read Data Visualize and Investigate Sequence Read Alignments When to Use the NGS Browser to Visualize and Investigate Data Open the NGS Browser Import Data into the NGS Browser Zoom and Pan to a Specific Region of the Alignment View Coverage of the Reference Sequence View the Pileup View of Short Reads Compare Alignments of Multiple Data Sets View Location, Quality Scores, and Mapping Information Flag Reads Evaluate and Flag Mismatches View Insertions and Deletions View Feature Annotations Print and Export the Browser Image Count Features from NGS Reads Identifying Differentially Expressed Genes from RNA-Seq Data Visualize NGS Data Using Genomics Viewer App Open the App Add Tracks by Importing Data Visualize Single Nucleotide Variation in Cytochrome P450 Sequence Analysis Exploring a Nucleotide Sequence Using 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 Exploring a Nucleotide Sequence Using the Sequence Viewer App Overview of the Sequence Viewer Importing a Sequence into the Sequence Viewer Viewing Nucleotide Sequence Information Searching for Words Exploring Open Reading Frames Closing the Sequence Viewer Explore a Protein Sequence Using the Sequence Viewer App Overview of the Sequence Viewer Viewing Amino Acid Sequence Statistics Closing the Sequence Viewer References Compare Sequences Using Sequence Alignment Algorithms Overview of Example Find a Model Organism to Study Retrieve Sequence Information from a Public Database Search a Public Database for Related Genes Locate Protein Coding Sequences Compare Amino Acid Sequences View and Align Multiple Sequences Overview of the Sequence Alignment App Visualize Multiple Sequence Alignment Adjust Sequence Alignments Manually Rearrange Rows Generate Phylogenetic Tree from Aligned Sequences Microarray Analysis Managing Gene Expression Data in Objects Representing Expression Data Values in DataMatrix Objects Overview of DataMatrix Objects Constructing DataMatrix Objects Getting and Setting Properties of a DataMatrix Object Accessing Data in DataMatrix Objects Representing Expression Data Values in ExptData Objects Overview of ExptData Objects Constructing ExptData Objects Using Properties of an ExptData Object Using Methods of an ExptData Object References Representing Sample and Feature Metadata in MetaData Objects Overview of MetaData Objects Constructing MetaData Objects Using Properties of a MetaData Object Using Methods of a MetaData Object Representing Experiment Information in a MIAME Object Overview of MIAME Objects Constructing MIAME Objects Using Properties of a MIAME Object Using Methods of a MIAME Object Representing All Data in an ExpressionSet Object Overview of ExpressionSet Objects Constructing ExpressionSet Objects Using Properties of an ExpressionSet Object Using Methods of an ExpressionSet Object Visualizing Microarray Images Overview of the Mouse Example Exploring the Microarray Data Set Spatial Images of Microarray Data Statistics of the Microarrays Scatter Plots of Microarray Data Phylogenetic Analysis Using the Phylogenetic Tree App Overview of the Phylogenetic Tree App Opening the Phylogenetic Tree App File Menu Tools Menu Window Menu Help Menu