CMBI - bioinformatics

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 nameDescription
BioVennWeb application for the comparison and visualization of biological lists using area-proportional Venn diagrams
Web tool for comparative metagenomics using cross-assembly
EXProtDatabase for proteins with an experimentally verified function
Genetic code prediction tool FACIL: Fast and Accurate genetic Code Inference and Logo
GeneSeekerPrediction of human disease genes
gpcrdbGPCRDB: Information system for G protein-coupled receptors (GPCRs)
LOFT Orthology prediction at scalable resolution by phylogenetic tree analysis
MGVMicrobial Genome Viewer
MimMinerComparing human disease phenotypes

Molden is a package for displaying Molecular Density.

MRSDatabase search and retrieval system
PAMRoll your own PAM Matrix
PhylopatWeb interface for querying Ensembl genomes using phylogenetic patterns
PinkThingTool to put genome-wide experiments in a genomic context
PredictProtein Service for sequence analysis and structure prediction
PyrobaseScreening of the genomes of Pyrococcus abyssi, Pyrococcus furiosus and Pyrococcus horikoshii
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
dBlastThe 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 IFWHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc.
YasaraYASARA 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 your ChIP profiles using this tool for unsupervised clustering and alignment