Bioinformatics Toolbox

Data Import and Application Deployment

File Formats and Database Access

You can access standard file formats for biological data, online databases, and Web sites. Bioinformatics Toolbox enables you to:

  • Read sequence data from standard file formats, including FASTA, PDB, and SCF
  • Read microarray data from file formats such as Affymetrix DAT, EXP, CEL, CHP, and CDF files; ImaGene® results format data; Agilent® Feature Extraction Software files; and GenePix® GPR and GAL files
  • Read data from online databases such as GenBank, EMBL, NCBI BLAST, and PDB
  • Import data directly from the NCBI Gene Expression Omnibus website with a single command
  • Read cytogenetic banding information from NCBI ideograms or UCSC cytoband text files
  • Read mass spectrometry data from MZXML and JCAMP-DX files

Sharing Algorithms and Deploying Applications

MATLAB provides tools that let you turn your data analysis program into a customized software application. These include development tools for building user interfaces, a visual integrated development environment, and a profiler. MATLAB application deployment products let you integrate your MATLAB algorithms with existing C, C++, and Java applications, deploy the developed algorithms and custom interfaces as standalone applications, convert MATLAB algorithms into Microsoft® .NET or COM components that can be accessed from any COM-based application, and create Microsoft Excel® add-ins.

You can integrate MATLAB with commonly used bioinformatics tools such as BioPerl, SOAP-based Web services, and COM plug-ins.


Calling BioPerl Functions from MATLAB
Pass arguments from MATLAB to Perl scripts and pull BLAST search data back to MATLAB.

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Physiologically-based Modeling of Oral Drug Absorption with SimBiology

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