Bioinformatics and Protein MS group software
Below are a list of software that have been developed or are frequently used at the Lowy Cancer Research Centre.
Software from Bioinformatics and Protein MS group
| 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, MSE, CDA) from shotgun proteomics data. |
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| FluTyper | Typing and subtyping of influenza virus from high-resolution mass maps using naïve Bayes classifiers and proteolytic signature peptides. |
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| MMSAT | Metabolite Mass Spectrometry Analysis tool. Web interface for processing targeted (SRM/MRM, precusor ions scanning) and untargetted metabolomic LC/GC-MS data. |
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| LPCHP | Linear predictive coding of histone modifications measured by ChIP-seq. The current standard method for the analysis of ChIP-seq data (in particular histone ChIP) is through the use of read count as a quantitative measure. LPCHP has been designed to capture features of signal profiles from to enable their use for downstream analysis. |
Software previously developed by Jason Wong
| 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 SpecAlign was developed by Dr Jason Wong at the University of Oxford, but the original webpage is no longer maintained.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). Command line version (specAlign1.21.tar.gz ) and Matlab versions (PAFFT.m & RAFFT.m) |
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| msmsEval | Tandem mass spectral quality assignment for high-throughput proteomics. The software analyses tandem mass spectral data from peptide LC-MS/MS experiments and empirically assigns a likelihood for the spectrum to be identifiable by peptide MS/MS search engines downstream. It is particularly useful for filtering poor quality spectra and also find high-quality spectrum that are unannotatible by search algorthms and therefore good candidates for representing peptides with post-translational modifications, etc. The source code for msmsEval is avaliable here (msmseval.tar.bz2). Note that this version now contains a parameter file for Orbitrap/FTICR data. |
Software frequently used
| ACPF | The Australian Proteomics Computational Facility has been established to provide a single advanced computing cluster accessible to scientists at proteomics centres all over Australia. |
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| InsPecT | Online peptide tandem mass spectra annotation algorithm. Allows the upload of custom databases. |
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| Galaxy | Online platform for the manipulation and analysis of biological datasets. Especially useful for multiple alignments, compare genomic annotations, profile metagenomic samples and linking with the UCSC browser(Aust mirror), etc. |
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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. |