Bioinformatics platform
The following links are to software and databases (co)-developed by VIB-researchers. The applications currently hosted are:
SOFTWARE
a) DNA-sequence analysis and primer design
SNPbox: allows highly standardized and automated primer design for large-scale SNP amplification and sequencing projects
SPADS: SPADS (Specific Primer and Amplicon Design Software) is a tool for the design of specific GSTs (Gene Specific Tags)
novoSNP: a program to find variations (SNPs and short INDELs) in resequencing projects.
SpliceMachine: The SpliceMachine server recognizes GT-AG splice sites on Arabidopsis thaliana and human DNA sequences.
b) Protein-sequence and -structure analysis
TANGO: predicts sequence dependent and mutational effects on the aggregation of peptides and proteins
FoldX: an atomic force field for calculating protein stability, dynamics and folding pathways, especially suited for predicting the effect of point mutations on these properties
ASaturA: an application that discriminates amino acid substitutions with high and low probabilities of occurrence
Untangle: a program designed to separate overlapping diffraction patterns from a set of crystals with slightly different orientations
c) Micro-array and gene expression analysis
GenTχWarper: an application tool for alignment, analysis and mining of gene expression time series
Toucan2: a workbench for regulatory sequence analysis on metazoan genomes : comparative genomics, detection of significant transcription factor binding sites, and detection of cis-regulatory modules (combinations of binding sites) in sets of coexpressed/coregulated genes
d) Phylogenetics and comparative genomics
TREECON: a software package for the construction and drawing of evolutionary trees in Windows
ADHoRe: ADHoRe (Automatic Detection of Homologous Regions) is a software tool that automatically detects genomic regions with statistically significant conserved gene content and order
i-ADHoRe: a highly sensitive software tool to detect degenerated homology relations within and between different genomes
HyperGeny: HYPERbolic phyloGENY viewer allows hyperbolic visualisation of very large tree structures
ZT: performs simple and partial Mantel tests
e) Sequence alignments and formatting
Align-m: a program for multiple alignments, also suitable for highly divergent sequences
ForCon: a user-friendly software tool for the conversion of nucleic acid and amino acid sequence alignments
DBToolkit: a broad suite of user-friendly tools to parse sequence databases into derived, FASTA-formatted sequence databases
f) Data integration and systems biology
ENDEAVOUR: a software application for the computational prioritisation of `test genes', based on a set of `training genes'. The ranking of a test gene is based on its similarity with the training genes, using several information sources (literature, gene expression data, BLAST, protein interactions, GO,...)
BINGO: a tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. Functions as a Cytoscape-plugin
SIM-plex: simulates genetic networks and allows genetic network construction while avoiding complex biochemical differential equations
g) Various
AFLPinSilico: performs AFLP simulations with different combinations of restriction enzymes or selective nucleotides, on organisms or data sets for which DNA sequences are available
Randfold: computes the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences
DATABASES
SNPeffect: database with non-synonymous SNPs and their predicted effect on the functional and physicochemical properties of the affected proteins
Alzheimer Disease & Frontotemporal Dementia Mutation Database: aims at collecting all known mutations and non-pathogenic coding variations in the genes related to Alzheimer disease (AD) and frontotemporal dementia
Inherited Peripheral Neuropathies Mutation Database: aims at collecting all mutations related to Inherited Peripheral neuropathies (IPN)
The European Ribosomal RNA Database: database which compiles all complete or nearly complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences
SPPG: Sequence platform for the Phylogenetic analysis of Plant Genes: an integrated sequence repository that combines EST sequence data with protein information from 32 different plant species
PlantCARE: a plant cis-acting regulatory element database
PRIDE: the proteomics identifications database
ADAN: a database of putative ligands for the most well-known modular protein-protein interaction domains like SH3, PDZ, etc. Many of these domains have a large number of homologues of which only a small fraction has been crystallized and only limited number of ligands is known. Based on the known structures, the ADAN project creates full atomic models of unknown protein-ligand structures using the FoldX algorithm and predicts new putative binders