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Bioinformatics Toolbox Examples

High-Throughput Sequencing

Exploring Genome-wide Differences in DNA Methylation ProfilesScript
Identifying Differentially Expressed Genes from RNA-Seq DataScript
Exploring Protein-DNA Binding Sites from Paired-End ChIP-Seq DataScript
Working with Illumina®/Solexa Next-Generation Sequencing DataScript
Performing a Metagenomic Analysis of a Sargasso Sea SampleScript
Analyzing the Human Distal Gut MicrobiomeScript

Sequence Analysis

Calculating and Visualizing Sequence StatisticsScript
Aligning Pairs of SequencesScript
Working with Whole Genome DataScript
Comparing Whole GenomesScript
Assessing the Significance of an AlignmentScript
Using Scoring Matrices to Measure Evolutionary DistanceScript
Using HMMs for Profile Analysis of a Protein FamilyScript
Building a Phylogenetic Tree for the Hominidae SpeciesScript
Analyzing the Origin of the Human Immunodeficiency VirusScript
Analyzing Synonymous and Nonsynonymous Substitution RatesScript
Investigating the Bird Flu VirusScript
Reconstructing the Origin and the Diffusion of the SARS EpidemicScript
Bootstrapping Phylogenetic TreesScript
Exploring Primer DesignScript
Identifying Over-Represented Regulatory MotifsScript
Predicting and Visualizing the Secondary Structure of RNA SequencesScript
Predicting Protein Secondary Structure Using a Neural NetworkScript

Microarray Data Analysis

Working with Objects for Microarray Experiment DataScript
Analyzing Illumina® Bead Summary Gene Expression DataScript
Detecting DNA Copy Number Alteration in Array-Based CGH DataScript
Analyzing Array-Based CGH Data Using Bayesian Hidden Markov ModelingScript
Visualizing Microarray DataScript
Gene Expression Profile AnalysisScript
Gene Ontology Enrichment in Microarray DataScript
Working with Affymetrix® DataScript
Preprocessing Affymetrix® Microarray Data at the Probe LevelScript
Exploring Gene Expression DataScript
Analyzing Affymetrix® SNP Arrays for DNA Copy Number VariantsScript
Working with GEO Series DataScript

Mass Spectrometry Data Analysis

Preprocessing Raw Mass Spectrometry DataScript
Visualizing and Preprocessing Hyphenated Mass Spectrometry Data Sets for Metabolite and Protein/Peptide ProfilingScript
Identifying Significant Features and Classifying Protein ProfilesScript
Differential Analysis of Complex Protein and Metabolite Mixtures using Liquid Chromatography/Mass Spectrometry (LC/MS)Script
Genetic Algorithm Search for Features in Mass Spectrometry DataScript
Batch Processing of Spectra Using Sequential and Parallel ComputingScript

Visualization Tools

Working with Graph Theory FunctionsScript
Working with the Clustergram FunctionScript
Visually Representing Interconnected DataScript
Visualizing the Three-Dimensional Structure of a MoleculeScript

Using MATLAB With Other Applications

Calling Bioperl Functions from MATLAB®Script
Connecting to Local DatabasesScript
Accessing NCBI Entrez Databases with E-UtilitiesScript
Connecting to the KEGG API Web ServiceScript
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