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CBS Prediction Servers

This page is the main entry to the on-line prediction services at CBS. All the servers are available as interactive input forms. In order to view the full documentation and use a server click on the appropriate link in the list below. The access to all the servers is free and unlimited for all academic users. For other users the access is also free but limited (see the details of the access policy).

Most of the servers are also available as stand-alone software packages to install and run at the user's site, with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms. Activate the 'Download' tab above to download software. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. Activate the 'SOAP WS' tab above for instructions on how to access the servers with SOAP.

On this page all the available options for a given service become visible on mouse over the name of the service.


NUCLEOTIDE SEQUENCES

Whole genome visualization and analysis

« GenomeAtlas
DNA structural atlases for complete microbial Genomes

Gene finding and splice sites

« EasyGene
Genes in prokaryotes
« EasyGene
Genes in prokaryotes
« HMMgene
Genes in eukaryotes
 MetaRanker
Identification of risk genes in complex phenotypes
 NetAspGene
Intron splice sites in Aspergillus DNA
« NetGene2
Intron splice sites in human, C. elegans and A. thaliana DNA
 NetPlantGene
Intron splice sites in Arabidopsis thaliana DNA
« NetStart
Translation start in vertebrate and A. thaliana DNA
 NetUTR
Splice sites in 5' UTR regions of human genes
« Promoter
Transcription start sites in vertebrate DNA
« RNAmmer
Ribosomal RNA sub units
« RNAmmer
Ribosomal RNA sub units

Analysis of DNA microarray data

 GenePublisher
Analysis of DNA microarray data
« OligoWiz
Design of oligonucleotides for DNA microarrays

Genomic epidemiology

 KmerFinder
Prediction of bacterial species using a fast K-mer algorithm
 MLST
Multi Locus Sequence Typing (MLST) from an assembled genome or from a set of reads
 NDtree
Phylogenic tree from reads using nucleotide difference method
 PathogenFinder
Prediction of a bacteria's pathogenicity towards human hosts
 ResFinder
Identifcation of acquired antibiotic resistance genes
 snpTree
SNPs phylogenetic tree from assembled genomes or sets of reads
 Tapir
Fast DNA search engine





SMALL MOLECULES

« ChemProt
Chemical-protein interactions
« hERG
Cardiotoxicity of drugs
 pHSol
pH-dependent aqueous solubility of druglike molecules
 

AMINO ACID SEQUENCES

Protein sorting

ChloroP »
Chloroplast transit peptides and their cleavage sites in plant proteins
LipoP »
Signal peptidase I & II cleavage sites in gram- bacteria
NetNES »
Leucine-rich nuclear export signals (NES) in eukaryotic proteins
SecretomeP »
Non-classical and leaderless secretion of proteins
SignalP »
Signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences
TargetP »
Subcellular location of proteins: mitochondrial, chloroplastic, secretory pathway, or other
TatP »
Twin-arginine signal peptides

Post-translational modifications of proteins

DictyOGlyc 
O-(alpha)-GlcNAc glycosylation sites (trained on Dictyostelium discoideum proteins)
NetAcet 
N-terminal acetylation in eukaryotic proteins
NetCGlyc »
C-mannosylation sites in mammalian proteins
NetCorona 
Coronavirus 3C-like proteinase cleavage sites in proteins
NetGlycate »
Glycation of ε amino groups of lysines in mammalian proteins
NetNGlyc »
N-linked glycosylation sites in human proteins
NetOGlyc »
O-GalNAc (mucin type) glycosylation sites in mammalian proteins
NetPhorest 
Linear motif atlas for phosphorylation-dependent signaling
NetPhos »
Generic phosphorylation sites in eukaryotic proteins
NetPhosBac 
Generic phosphorylation sites in bacterial proteins
NetPhosK 
Kinase specific phosphorylation sites in eukaryotic proteins
NetPhosYeast 
Serine and threonine phosphorylation sites in yeast proteins
NetPicoRNA 
Posttranslational cleavage by picornaviral proteases
NetworKIN 
In vivo kinase-substrate relationships
ProP »
Arginine and lysine propeptide cleavage sites in eukaryotic protein sequences
YinOYang »
O-(beta)-GlcNAc glycosylation and Yin-Yang sites (intracellular/nuclear proteins)

Immunological features

BepiPred »
Linear B-cell epitopes
DiscoTope »
Discontinuous B-cell epitopes
HLArestrictor 
Patient-specific HLA restriction elements and optimal epitopes within peptides
MHCcluster 
MHC class 1 clustring based on binding specififcity
NetChop »
Proteasomal cleavages (MHC ligands)
NetCTL »
Integrated class I antigen presentation
NetCTLpan »
Pan-specific integrated class I antigen presentation
NetMHC »
Binding of peptides to MHC class I alleles
NetMHCcons »
Binding of peptides to any known MHC class I molecule
NetMHCII »
Binding of peptides to MHC class II alleles
NetMHCIIpan »
Pan-specific binding of peptides to MHC class II HLA-DR alleles of known sequence
NetMHCpan »
Pan-specific binding of peptides to MHC class I alleles of known sequence
NetMHCstab 
Stability of peptide:MHC-I complexes
NNAlign 
Identifying sequence motifs in quantitative peptide data
VDJsolver »
Analysis of human immunoglobulin VDJ recombination

Protein function and structure

ArchaeaFun 
Enzyme/non-enzyme and enzyme class (Archaea)
CPHmodels 
Protein structure from sequence: distance constraints
distanceP 
Protein distance constraints
EPipe »
Functional differences of protein variants
InterMap3D 
Co-evolving amino acids in proteins
NetSurfP »
Protein secondary structure and relative solvent accessibility
NetTurnP 
β-turns and β-turn types in proteins
ProtFun »
Protein functional category and enzyme class (Eukarya)
RedHom 
Reduction of sequence similarity in a data set
SigniSite 
Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments
TMHMM »
Transmembrane helices in proteins
VarDom 
Domains in the malaria antigen family PfEMP1