UNSW Cancer Research Centre - UNSW CRC Bioinformatics

Below are a list of software that have been developed or are frequently used at the UNSW Cancer Research Centre.

Software from UNSW CRC

Disulfide Analysis	Automated analysis of disulfide bonds from PDB files. Provides a simple web interface for obtaining geometric measures, solvent accessibility values, secondary structural information and classification of disulfide bonds.
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ETISEQ	Software for processing concurrently fragmented peptide mass spectra (i.e. parallel CID, MS^E, CDA) from shotgun proteomics data.

Software frequently used

SpecAlign	Preprocessing and visualisation software for spectral and chormatographic datasets. Specially designed for the alignment of SELDI-MS data, but also frequently used for the processing of metabolomics type data. SpecAlign was developed by Dr Jason Wong at the University of Oxford, but the original webpage is no longer maintained. An updated version (2.4.1) has been recently been released and can be downloaded here (release notes).
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InsPecT	Online peptide tandem mass spectra annotation algorithm. Allows the upload of custom databases.
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GenePattern	Integrated online platform with tools for gene expression analysis, proteomics, SNP analysis and other data processing tasks.
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DAVID	Database for Annotation, Visualization and Integrated Discovery. Used for functional clustering of gene lists based on gene ontology and other keywords.