Workshop in Computational
Bioskills - Spring 2010
Lesson 6 - Matlab bioinformatix toolbox and working with databases (MySql)
Part
1 - Matlab - Workspace, docs and demos
Part
2 - Bioinformatix ToolBox
Part
3 - Databases MySql - Short introduction
Part 4 - Perl's MySQL interface
Part 5 - PHP's MySQL interface
Part 6 - Working with databases in Matlab
Bioinformatics Toolbox
The toolbox provides access to genomic and proteomic data formats, analysis techniques,
and specialized visualizations for genomic and proteomic sequence and microarray analysis.
Overview:
- Capabilities for microarray data analysis and visualization
- Normalization, Gene filters, clustering,...
- Support for mass spectrometry preprocessing and analysis
- Graph theory and graph visualization tools
- Statistical learning functionality
- Feature selection, classification (e.g. SVM), cross validation,...
- Gene Ontology functionality
- Sequence analysis tools
- including functions for pairwise and multiple sequence alignment
- Phylogenetic tree analysis tools
Tree buidling, interactive tree view
- Genomic, proteomic, and gene expression file formats FASTA, PDB, Affymatrix,...
Access to Web-based databases - Directly connect: GeneBank, PDB, EMBL, BLAST,...
In the toolbox you can find useful tutorials and demos demonstrating how to use the tools.
Working with Databases using Matlab
- Matlab has a Database ToolBox, enabling to work with various databases management systems including Sql commands
- Bioinformatix Databses Toolbox : provides functions to directly access many standard Web-based databases such as GenBank, EMBL, PIR, and PDB. See a tutorial here