Many of the bioinformatics services that used to be available at the CMBI are now available via the website of DTL, the DTL Data programme of the Dutch Techcentre for Life Sciences .

Services currently available at the CMBI

Service name Description
BioVenn Web application for the comparison and visualization of biological lists using area-proportional Venn diagrams
crAss Web tool for comparative metagenomics using cross-assembly
EXProt Database for proteins with an experimentally verified function
FACIL Genetic code prediction tool FACIL: Fast and Accurate genetic Code Inference and Logo
GeneSeeker Prediction of human disease genes
gpcrdb GPCRDB: Information system for G protein-coupled receptors (GPCRs)
LOFT Orthology prediction at scalable resolution by phylogenetic tree analysis
MGV Microbial Genome Viewer
MimMiner Comparing human disease phenotypes

Molden is a package for displaying Molecular Density.

MRS Database search and retrieval system
PAM Roll your own PAM Matrix
Phylopat Web interface for querying Ensembl genomes using phylogenetic patterns
PinkThing Tool to put genome-wide experiments in a genomic context
PredictProtein Service for sequence analysis and structure prediction
Pyrobase Screening of the genomes of Pyrococcus abyssi, Pyrococcus furiosus and Pyrococcus horikoshii
Signature Characterize sequences using taxonomic signature genes (complementary to sequence-based classification)

Packages currently available at the CMBI

This table gives you an overview of the packages developed at the CMBI. Some packages are freely availably, others can be ordered, more information can be found at the package site.

Package name Description
dBlast The DBLAST package is a wrapper for distributed NCBI BLAST, and was designed to run BLAST on Beowulf clusters, SMP machines, and MOSIX machines, without the need to buy/build/use a parallel BLAST version (MPI/PVM...).
Molden MOLDEN a pre- and post processing program of molecular and electronic structure
WHAT IF WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc.
Yasara YASARA is an interactive real-time molecular dynamics program, covering a wide range of topics in the rapidly growing field of structural bioinformatics: Molecular modeling, protein folding (based on any amount of information available: from sequence alone to fully assigned NMR spectra), docking and parallel macromolecular dynamics.
Queen QUEEN, a software package for the quantitative evaluation of experimental NMR restraints.
CATCH CATCH your ChIP profiles using this tool for unsupervised clustering and alignment