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DTU HEALTH TECH
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Services
Gene finding and splice sites
EasyGene
Gene finding in prokaryotes
HMMgene
Prediction of vertebrate and C. elegans genes
NetAspGene
Intron splice sites in Aspergillus DNA
NetGene2
Intron splice sites in human, C. elegans and A. 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
Genomic epidemiology
CSI Phylogeny
CSI Phylogeny calls SNPs, filters the SNPs, does site validation and infers a phylogeny
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
NDtreePhylogenic tree from reads using nucleotide difference method
PathogenFinder
Prediction of a bacteria's pathogenicity towards human hosts
ResFinder
Identifcation of acquired antibiotic resistance genes
Immunological features
ArrayPitope
Residue-level epitope mapping of antigens based on peptide microarray data
BepiPred
Prediction of potential B-cell epitopes from protein sequence
DiscoTope
Improved B-cell epitope prediction using AlphaFold2 modeling and inverse folding latent representations
LYRA
Lymphocyte receptor automated modelling
MAIT Match
Calculate similarity between CDR3 sequences and a reference database of MAIT sequences
MHCMotifDecon
Motif deconvolution of Multi-allele immunopetidomics data
MHCcluster
MHC clustring based on binding specififcity
MuPeXI
Prediction of neo-epitopes from tumor sequencing data
NNAlign
Discovering sequence motifs in biological sequences
NetAllergen
Protein allergenicity prediction
NetBoLAIIpan
Prediction of peptide interactions with bovine MHC Class II BoLA-DRB3 molecules
NetCTL
Predection of CTL epitopes in protein sequences
NetCTLpan
Pan-specific integrated class I antigen presentation
NetChop
Proteasomal cleavages (MHC ligands)
NetH2pan
Prediction of peptide interactions with murine MHC class I (H2) molecules.
NetMHC
NetMHC: Binding of peptides to MHC class I molecules
NetMHCII
Binding of peptides to MHC class II molecules
NetMHCIIpan
Pan-specific binding of peptides to MHC class II molecules of known sequence
NetMHCcons
Binding of peptides to any known MHC class I molecule
NetMHCpan
Pan-specific binding of peptides to MHC class I proteins of known sequence
NetMHCpanExp
Pan-specific binding of peptides to MHC class I proteins of known sequence including antigen expression
NetMHCphosPan
Pan-specific binding of phosphorylated peptides to HLA class I molecules.
NetMHCstabpan
Pan-specific stability of peptide:MHC-I complexes
NetPolyEV
Construction of Polytope Vaccines
NetTCR
Sequence-based prediction of peptide-TCR binding.
NetTepi
T-cell epitopes restricted to prevalent HLA-A and HLA-B molecules
PickPocket
Binding of peptides to any known MHC class I molecule using binding pocket matrix extrapolation
PopCover
Selection of MHC epitopes for optimal population and pathogen coverage
TCRbase
Sequence similarity-based prediction of peptide-TCR binding.
TCRpMHCmodels
Structural modeling tool of TCR-pMHC class I complexes
VDJSolver
Analysis of human immunoglobulin VDJ recombination
Post-translational modifications of proteins
DictyOGlyc
O-(alpha)-GlcNAc glycosylation sites (trained on Dictyostelium discoideum proteins)
NetCGlyc
C-mannosylation sites in mammalian proteins
NetGPI
GPI Anchor predictions
NetNGlyc
N-linked glycosylation sites in human proteins
NetOGlyc
O-GalNAc (mucin type) glycosylation sites in mammalian proteins
NetPhos
Generic phosphorylation sites in eukaryotic proteins
NetPhosBac
Generic phosphorylation sites in bacterial proteins
NetPhosYeast
Serine and threonine phosphorylation sites in yeast proteins
NetPhospan
Prediction of phosphorylation using convolutional neural networks (CNNs).
NetworKIN
In vivo kinase-substrate relationships
ProP
Arginine and lysine propeptide cleavage sites in eukaryotic protein sequences
Protein function and structure
Cofactory
Identification of Rossmann folds and prediction of FAD, NAD and NADP specificity
DeepTMHMM
Prediction of transmembrane helices in proteins
NetSolP
Prediction of solubility and usability of proteins expressed in E. coli
NetSurfP
Protein secondary structure and relative solvent accessibility
NetTurnP
Amino acid predection in β-turns and β-turn types in proteins
SigniSite
Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments
TMHMM
Prediction of transmembrane helices in proteins
VarDom
Domains in the malaria antigen family PfEMP1
VirtualPulldown
Create protein physical interaction networks using the InWeb 3.0/5.0 inferred human interactome
DistanceP
Predicts protein distance constraints
Protein sorting
DeepLoc
Prediction of eukaryotic protein subcellular localization using deep learning
DeepLocPro
Prediction of prokaryotic 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
Prediction of non-classical protein secretion
SignalP
Prediction of Signal Peptides and their cleavage sites in all domains of life
TargetP
Subcellular location of proteins: mitochondrial, chloroplastic, secretory pathway, or other
TatP
Presence and location of Twin-arginine signal peptides
Miscellaneous
AnOxPePred
Prediction of antioxidative properties of peptides using convolutional neural network
Barracoda
Analysing DNA barcode sequencing data
ClusteringTool
Clustering of peptide data
HaploCart
HaploCart is a human haplogroup prediction algorithm for NGS data or mitogenomes in FASTA format
TumorTracer
Tissue of origin of tumors from genomics data
pHSol
pH-dependent aqueous solubility of druglike molecules
Bioinformatics Tools
AMUSER
Designing optimal primers for USER fusion.
Blast2logo
Generation of sequence-profile logos using PSI-blast.
CMG-biotools
Comparative Microbial Genomics biotools
EasyGibbs
Motif recognition in protein sequences by Gibbs sampler.
EasyPred
Development of neural network and weight matrix prediction methods for protein sequences.
FeatureExtract
Extraction of sequence and annotation, e.g. intron/exon structure, from GenBank format files
GibbsCluster
Simultaneous alignment and clustering of peptide data
MHCMotifViewer
Easy browsing and visualisation of MHC class I and II binding motifs.
MatrixPlot
Visualizing structural sequence constraints.
MaxAlign
Maximizing the size of gap-free columns by selecting an optimal subset of sequences in an alignment.
RedHom
Reduction of sequence similarity in a data set
RevTrans
Multiple alignment of coding DNA using protein level information
Seq2Logo
Sequence logo generator
TreeHugger
Constructing NJ or UPGMA trees from DNA and Protein alignments.
VirtualRibosome
A comprehensive tool for translating DNA sequences to the corresponding peptide sequences.
Jetset
Selecting an optimal microarray probe set to represent a gene
Datasets
AraClean
Arabidopsis thaliana data set
CellCycle
Cell cycle related data sets and supplementary information
DNA2protSS
mRNA sequences and the corresponding protein secondary structure assignments
DOGS
Database Of Genome Sizes
GlycateBase
Database of glycation data for ε amino groups of lysines
MetaGenomic Species
Information on metagenomic species (MGS)and co-abundance gene groups (CAGs) of the human gut
NESbase
Database of nuclear export signals
NetStart
Translation initiation site data sets
OglycBase
Database of O-glycosylated proteins
Phosphobase
Database of phosphorylation sites, has moved to EMBL
PlantExpr
Supplementary plant gene expression data for scientific publications
SignalP datasets
Signal peptide data sets