matlab for bioinformatics

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MATLAB Applications in Bioinformatics

Developing and Deploying Bioinformatics

Applications with MATLAB

The MathWorks, Inc.

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Presentation Layout

 MATLAB applications in Bioinformatics

 Customer success stories

 MATLAB & The Bioinformatics Toolbox

 Sequence analysis

 Microarray analysis

 Integrating MATLAB with other tools

 MATLAB as computational engine for Excel

 Questions/Answers & Wrap-up

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Bioinformatics Applications

• Sequence analysis

• Base calling algorithm design, sequence alignment,

sequence building algorithms

• Microarray analysis

• Image processing, QA/QC, data normalization, data analysis

• Proteomics

• Mass Spectrometry signal processing, protein marker

identification and classification, peptide sequence

identification, 2D-Gel image analysis

• Systems Biology

• Interaction network identification, simulation of metabolic

pathways, flux analysis

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Bioinformatics teams supporting multiple

constituencies with multiple tools.

• SPLUS, R, SAS, Mathematica

• Web based tools

•Custom one-off analyses

•Programs for biologists

Software Engineers

•C++, Java

•Work off MATLAB prototypes

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Using MATLAB, bioinformatics teams can support

multiple constituencies.

MATLAB GUI’s, analyses

•Custom one-off analyses

•Programs for biologists

Applicatio ns

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Complete draft of the human genome, accelerated by Applied Biosystems — using MATLAB

algorithms.

“Having one integrated package

is a big advantage Using MATLAB and the MATLAB Compiler reduced my development time by a factor of 4 or 5.”

“MATLAB has always been ideal as an algorithm prototyping tool,” Labrenz concludes, “but the MATLAB Compiler and C/C++ Math and Graphics Libraries add a whole new dimension, allowing rapid

delivery of sophisticated solutions.”

Jim Labrenz, Applied Biosystems

User example: Genetic Sequence Base Calling

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User example: Breast Cancer Prognosis

Rosetta Inpharmatics recently developed a tool that enables clinicians to determine a breast cancer patient’s prognosis based on the gene expression profile of the primary tumor

“Since MATLAB and the Image Processing Toolbox are fully integrated and the MATLAB platform is very good for matrix calculation, we did not have

to spend time writing the low level image processing and the basic data analysis routines like vector and matrix calculations”

“Our research scientists are happy with the quick feedback,” Dr Dai says “Using MathWorks tools,

we can respond to their requests very fast, and it’s easy for the scientists to use these tools

Using the GUIs that we develop in MATLAB, they can access functions without having to remember the underlying code.”

Dr Hongyue Dai, Rosetta Inpharmatics/Merck & Company

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More than 600 textbooks for education and professional use, in 19

– Natural Sciences – Environmental Sciences

Thousands of universities teach students using

MathWorks products.

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Industry Issues & Solutions

•Integrating tools from various

programming languages is

difficult, closed source tools are

not customizable, and freeware

is often not supported

•There is no standard biological

data format

•Applications must be easily

deployable within organizations

•MATLAB is a supported, open architecture, user-friendly

environment for data analysis across applications, algorithm development, and deployment

•MATLAB and the Bioinformatics Toolbox provides file format support for common data sources (web-

based, sequences, microarray, etc.)

•MATLAB’s deployment tools and user-interface design environment allow easy deployment of MATLAB based applications

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The Bioinformatics Toolbox

Robert HensonThe MathWorks, Inc

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The MathWorks Product Family

Code Generation

Blocksets

Integrated for:

 technical computing, data analysis and visualization

 system modeling and simulation

 implementation of real-time embedded software

PC-based real-time systems

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• FASTA, PDB, SCF, GPR, GAL

• GenBank, EMBL, PIR, PDB

• Needleman-Wunsch, Smith-Waterman

• DNA/RNA/AA conversions, pattern searching

• Lowess, global mean, MAD (median absolute deviation)

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Command History

MATLAB Desktop Tools

Launchpad:

Start other tools and

demos

Workspace Browser:

See your data

Command Window

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Sequence Alignment Tutorial Example

• Get human and mouse genes from GenBank

• Look for open reading frames (ORFs)

• Convert DNA sequences to amino acid sequences

• Create a dotplot of the two sequences

• Perform global alignment

• Perform local alignment

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Microarray Data Analysis Tutorial Example

• Plot expression profiles for genes

• Filter genes based on information content of profile

• Perform hierarchical clustering

• Perform K-means clustering

• Perform Principal Component Analysis

Reference:

DeRisi, JL, Iyer, VR, Brown, PO "Exploring the metabolic and genetic control of gene expression on a genomic scale." Science 1997 Oct 24;278(5338):680-6.

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Integrating and Deploying Bioinformatics Tools with

MATLAB

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C/C++

Web

Stand-alone

Excel COM

Deploying with MATLAB

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Push Data into MATLAB

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Computational Engine for Excel

Spread Sheet Applications

• MATLAB Excel Link can be the

computational engine behind your

Excel applications

• Fast scalable solution

MLPutMatrix("data",B2:H43) MLPutMatrix("Genes",A2:A43) MLPutMatrix("TimeSteps",B1:H1) MLEvalString("clustergram(data,'RowLabels',…

Genes,'ColLabels',TimeSteps)")

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Image Processing Signal Processing

Statistics

What else could you do?

Bioinformatics

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