Contributed software
| Tool | Description | References |
|---|---|---|
| i-cisTarget | An integrative genomics method for the prediction of regulatory features (motifs and in vivo features), and cis-regulatory modules in Drosophila |
Manuscript in preparation |
| cisTargetX | Predict motifs and target genes in Drosophila, starting from a list of co-expressed genes. |
[1] |
| TOUCAN | Workbench for regulatory sequence analysis. Features include: detection of conserved sequences, motif discovery (MotifSampler, Oligo-analysis), motif matching (MotifLocator, MotifScanner), statistical over-representation, module discovery (ModuleSearcher), module matching (ModuleScanner), etc.
Launch Toucan (Java Web Start application) |
[2][3] |
| ENDEAVOUR / HIGHFLY |
ENDEAVOUR/HIGHFLY
Framework for the computational prioritisation of
genes by genomic data fusion, based on the similarity
with a set of training genes. This similarity takes into
account: scientific literature (MEDLINE abstracts), Gene
Ontology, KEGG pathways, InterPro domains, BIND protein
interactions, EST-based expression data, microarray gene
expression data, transcription factor binding sites, cis-regulatory
modules, and BLAST-based sequence similarity. Credits: Leo-Charles Tranchevent and Bert Coessens | [4][5][6] |
| ModuleSearcher and ModuleMiner |
Solve the combinatorial optimization problem to find the optimal combination of transcription factor binding sites in a set of co-regulated sequences.
ModuleSearcher and ModuleScanner are available within TOUCAN.
ModuleMiner is an extension of ModuleSearcher that increases CRM and target gene specificity by performing genome-wide optimizations. Credits: Peter Van Loo |
[7][8][9] |
Bioinformatics resource lists
| Name | Link | Description |
|---|---|---|
| EMBOSS | http://10.33.126.32/emboss-explorer/ | Local installation of the EMBOSS suite of bioinformatics tools (only accessible within the KULeuven firewall). Note: you can also use the standalone EMBOSS package on our linux server (request a user account). |
| Mobyle | http://mobyle.pasteur.fr/cgi-bin/portal.py | |
| Links directories | Directories of links to various bioinformatics tools and web services |
