Chief Investigators
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Bioinformatics Tools
Multiple Analytical Tools
The Visible Cell
Psychro Web Server, UNSW
Thomas Huber's Tools
WEHI Bioinformatics Software
Stream: Modeling, visualizing, and predicting the transcriptional regulation of a target gene
CONTOURv1: Cancer (Onco) geNes from disrupTed mOdUles and their Relationships
MCL-CAw: a refinement of MCL for protein complex detection
Bioinformatics Resource Australia-EML
Pattern Recognition
WOOF: A word-oriented objective function for validation of sequence alignments
MEME: Motif Discovery and MAST: Motif Search
DEME: Discriminatively Enhanced Motif Elicitation (Motif Discovery using Positive & Negative Examples)
GLAM2: Gapped Local Alignment of Motifs
GANN: Regulatory Region Identification
Cluster Buster: Finding Dense Clusters of Motifs in DNA Sequences
Feature Predictors
Protein Prowler: Subcellular Localisation Predictor
Golgi Transmembrane Protein Prediction
Support Vector Machines For Predicting Transmembrane Domains
Accessible Surface Area Prediction
Marcoil: HMM-based coiled-coil prediction program
Phat: finding genes in eukaryotic organisms
PoPS: Prediction of Protease Specificity
go2ppi: Prediction of protein-protein interactions
DISRUPT: Prediction of network disruptions
Visualisation
The iCluster SubCellular Localisation Image Visualiser
The DomainDraw Macromolecule Schematic Drawing Program
Imaging
The OBCOL imaging segmentation and colocalisation tool
Ontology
GO slim creation pipeline - The files and documents collected here are described in the manuscript “Automatic, context-specific generation of Gene Ontology slims” (MJ Davis, MS Sehgal and MA Ragan, BMC Bioinformatics 11:498, 2010)
Small Molecule Ontology - The files and documents collected here are described in the manuscript "A Semantic Web for small molecules and their biological targets" (JY Choi, MJ Davis, AF Newman and MA Ragan, Journal of Chemical Information and Modeling 50:732-741, 2010)
Sequence Tools
Mosaic: a visual framework for sequence analysis using n-grams and spectral rearrangement
decaf+py: DistancE Calculation using Alignment-Free methods in PYthon
Bellerophon - detect chimeric sequences in a multiple sequence dataset
Mapwhere: finds perfect or partial matches to motifs in (protein) sequences
Bellerophon - detect chimeric sequences in a multiple sequence dataset
The PoCM ("Possum") protein contact prediction server
Triplexator : detect nucleic acid triple helices
NorahDesk: a computational tool for detecting small non-coding RNA(ncRNA) from deep sequencing data (RNA-seq)
Phylogenetics
decaf+py: DistancE Calculation using Alignment-Free methods in PYthon
EvolSimulator: A simulation test bed for gene and genome evolution
EEEP: Efficient Evaluation of Edit Paths
PyEvolve: a toolkit for statistical molecular evolutionary analysis of genomes
Vestige: Maximum likelihood phylogenetic footprinting
Statistical Analysis
Microarray Missing Value Estimation Toolbox: estimates missing values by using correlation structure of the data
GONOME: Find over and under-represented GO Terms from a set of genomic positions
Log Rank Test
Testing between Curves
LIMMA: Linear Models for Microarray Data
StatMod: R Library for modelling and analysis
Databases and Datasets
Towards the mammalian interactome: inference of a core mammalian interaction set in mouse
Protein-protein interaction as a predictor of subcellular location
LGT144: Lateral genetic transfer datasets from the phylogenetic pipeline project
Synthetic eight-taxon & putative orthologs datasets
altExtron: a high quality data set of transcript confirmed introns and exons for human and other organisms
dBP: A class of human exons with predicted distant branch points
MmERV: information about the mouse retrovirus MmERV
LOCATE: Mouse Proteome Subcellular Localization Databases
PhosphoregDB: mammalian protein kinases and phosphatases
VariantDB
Spectrum Database: Proteomics
Barphlye: Bayesian analysis of rearrangement phylogeny in Yersinia
StaphGT:Modularity of lateral genetic transfer in Staphylococcus - Datasets
E. coli - Shigella 27 genomes LGT
QTL and Genetic Maps
agrfToMm: qtl data + genotyping data to a mapmaker-type input file
getMaps: shows matching map positions Whitehead, Marshfield, Genethon and Decode genetic maps
Quantitative Trait Haplotype Analysis: test for QTL association
Generate genetic maps for humans using physical and genetic maps
Other
Reordering genes: reorders a list of gene names according to their UniGene names
