CBS Prediction Servers

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.

NOTE: The SOAP-based Web Services available previously from this site are no longer maintained and have been deactivated.

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

NUCLEOTIDE SEQUENCES

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

« 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

Miscellaneous

Barracoda
Analysing DNA barcode sequencing data

TumorTracer
Tissue of origin of tumors from genomics data

SMALL MOLECULES

ChemProt
Chemical-protein interactions

NutriChem
Food-disease associations

pHSol
pH-dependent aqueous solubility of druglike molecules

AMINO ACID SEQUENCES

Protein sorting

ChloroP »
Chloroplast transit peptides and their cleavage sites in plant proteins

DeepLoc »
Prediction of eukaryotic protein subcellular localization using deep learning

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

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

ArrayPitope
Residue-level epitope mapping of antigens based on peptide microarray data

BepiPred »
Linear B-cell epitopes

DiscoTope »
Discontinuous B-cell epitopes

HLArestrictor
Patient-specific HLA restriction elements and optimal epitopes within peptides

LYRA
Lymphocyte receptor automated modelling

MHCcluster
MHC class 1 clustring based on binding specififcity

MuPeXI
Prediction of neo-epitopes from tumor sequencing data

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 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

NetMHCstabpan »
Pan-specific stability of peptide:MHC-I complexes

NetTepi »
T-cell epitopes restricted to prevalent HLA-A and HLA-B molecules

NNAlign »
Identifying sequence motifs in quantitative peptide data

PickPocket »
Binding of peptides to any known MHC class I molecule using binding pocket matrix extrapolation

VDJsolver »
Analysis of human immunoglobulin VDJ recombination

Protein function and structure

ArchaeaFun
Enzyme/non-enzyme and enzyme class (Archaea)

Cofactory »
Identification of Rossmann folds and prediction of FAD, NAD and NADP specificity

CPHmodels
Protein structure from sequence: distance constraints

distanceP
Protein distance constraints

FeatureP
Functional differences of protein variants

InterMap3D
Co-evolving amino acids in proteins

NetDiseaseSNP
Predicts whether a single non-synonymous SNP causes a disease or is invariant

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

ThermoP
Prediction of GH enzyme melting temperature at pH 5.0

TMHMM »
Transmembrane helices in proteins

VarDom
Domains in the malaria antigen family PfEMP1