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

« 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

Analysis of DNA microarray data

GenePublisher
Analysis of DNA microarray data

« OligoWiz
Design of oligonucleotides for DNA microarrays

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

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

TMHMM »
Transmembrane helices in proteins

VarDom
Domains in the malaria antigen family PfEMP1