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Gene finding and splice sites

  • EasyGeneGene finding in prokaryotes
  • HMMgenePrediction of vertebrate and C. elegans genes
  • NetAspGeneIntron splice sites in Aspergillus DNA
  • NetGene2Intron splice sites in human, C. elegans and A. thaliana DNA
  • NetStartTranslation start in vertebrate and A. thaliana DNA
  • NetUTRSplice sites in 5' UTR regions of human genes
  • PromoterTranscription start sites in vertebrate DNA

Genomic epidemiology

  • CSI PhylogenyCSI Phylogeny calls SNPs, filters the SNPs, does site validation and infers a phylogeny
  • KmerFinderPrediction of bacterial species using a fast K-mer algorithm
  • MLSTMulti Locus Sequence Typing (MLST) from an assembled genome or from a set of reads
  • NDtreeNDtreePhylogenic tree from reads using nucleotide difference method
  • PathogenFinderPrediction of a bacteria's pathogenicity towards human hosts
  • ResFinderIdentifcation of acquired antibiotic resistance genes

Immunological features

  • ArrayPitopeResidue-level epitope mapping of antigens based on peptide microarray data
  • BepiPredPrediction of potential B-cell epitopes from protein sequence
  • DiscoTopeImproved B-cell epitope prediction using AlphaFold2 modeling and inverse folding latent representations
  • LYRALymphocyte receptor automated modelling
  • MAIT MatchCalculate similarity between CDR3 sequences and a reference database of MAIT sequences
  • MHCMotifDeconMotif deconvolution of Multi-allele immunopetidomics data
  • MHCclusterMHC clustring based on binding specififcity
  • MuPeXIPrediction of neo-epitopes from tumor sequencing data
  • NNAlignDiscovering sequence motifs in biological sequences
  • NetAllergenProtein allergenicity prediction
  • NetBoLAIIpanPrediction of peptide interactions with bovine MHC Class II BoLA-DRB3 molecules
  • NetCTLPredection of CTL epitopes in protein sequences
  • NetCTLpanPan-specific integrated class I antigen presentation
  • NetChopProteasomal cleavages (MHC ligands)
  • NetH2panPrediction of peptide interactions with murine MHC class I (H2) molecules.
  • NetMHCNetMHC: Binding of peptides to MHC class I molecules
  • NetMHCIIBinding of peptides to MHC class II molecules
  • NetMHCIIpanPan-specific binding of peptides to MHC class II molecules of known sequence
  • NetMHCconsBinding of peptides to any known MHC class I molecule
  • NetMHCpanPan-specific binding of peptides to MHC class I proteins of known sequence
  • NetMHCpanExpPan-specific binding of peptides to MHC class I proteins of known sequence including antigen expression
  • NetMHCphosPanPan-specific binding of phosphorylated peptides to HLA class I molecules.
  • NetMHCstabpanPan-specific stability of peptide:MHC-I complexes
  • NetPolyEVConstruction of Polytope Vaccines
  • NetTCRSequence-based prediction of peptide-TCR binding.
  • NetTepiT-cell epitopes restricted to prevalent HLA-A and HLA-B molecules
  • PickPocketBinding of peptides to any known MHC class I molecule using binding pocket matrix extrapolation
  • PopCoverSelection of MHC epitopes for optimal population and pathogen coverage
  • TCRbaseSequence similarity-based prediction of peptide-TCR binding.
  • TCRpMHCmodelsStructural modeling tool of TCR-pMHC class I complexes
  • VDJSolverAnalysis of human immunoglobulin VDJ recombination

Post-translational modifications of proteins

  • DictyOGlycO-(alpha)-GlcNAc glycosylation sites (trained on Dictyostelium discoideum proteins)
  • NetCGlycC-mannosylation sites in mammalian proteins
  • NetCoronaCoronavirus 3C-like proteinase cleavage sites in proteins
  • NetGPIGPI Anchor predictions
  • NetNGlycN-linked glycosylation sites in human proteins
  • NetOGlycO-GalNAc (mucin type) glycosylation sites in mammalian proteins
  • NetPhosGeneric phosphorylation sites in eukaryotic proteins
  • NetPhosBacGeneric phosphorylation sites in bacterial proteins
  • NetPhosYeastSerine and threonine phosphorylation sites in yeast proteins
  • NetPhospanPrediction of phosphorylation using convolutional neural networks (CNNs).
  • NetworKINIn vivo kinase-substrate relationships
  • ProPArginine and lysine propeptide cleavage sites in eukaryotic protein sequences

Protein function and structure

  • CofactoryIdentification of Rossmann folds and prediction of FAD, NAD and NADP specificity
  • DeepTMHMMPrediction of transmembrane helices in proteins
  • NetSolPPrediction of solubility and usability of proteins expressed in E. coli
  • NetSurfPProtein secondary structure and relative solvent accessibility
  • NetTurnPAmino acid predection in β-turns and β-turn types in proteins
  • SigniSiteIdentification of residue-level genotype-phenotype correlations in protein multiple sequence alignments
  • TMHMMPrediction of transmembrane helices in proteins
  • VarDomDomains in the malaria antigen family PfEMP1
  • VirtualPulldownCreate protein physical interaction networks using the InWeb 3.0/5.0 inferred human interactome
  • DistancePPredicts protein distance constraints

Protein sorting

  • DeepLocPrediction of eukaryotic protein subcellular localization using deep learning
  • DeepLocProPrediction of prokaryotic protein subcellular localization using deep learning
  • LipoPSignal peptidase I & II cleavage sites in gram- bacteria
  • NetNESLeucine-rich nuclear export signals (NES) in eukaryotic proteins
  • SecretomePPrediction of non-classical protein secretion
  • SignalPPrediction of Signal Peptides and their cleavage sites in all domains of life
  • TargetPSubcellular location of proteins: mitochondrial, chloroplastic, secretory pathway, or other
  • TatPPresence and location of Twin-arginine signal peptides


  • AnOxPePredPrediction of antioxidative properties of peptides using convolutional neural network
  • BarracodaAnalysing DNA barcode sequencing data
  • HaploCartHaploCart is a human haplogroup prediction algorithm for NGS data or mitogenomes in FASTA format
  • TumorTracerTissue of origin of tumors from genomics data
  • pHSolpH-dependent aqueous solubility of druglike molecules

Bioinformatics Tools

  • AMUSERDesigning optimal primers for USER fusion.
  • Blast2logoGeneration of sequence-profile logos using PSI-blast.
  • CMG-biotoolsComparative Microbial Genomics biotools
  • EasyGibbsMotif recognition in protein sequences by Gibbs sampler.
  • EasyPredDevelopment of neural network and weight matrix prediction methods for protein sequences.
  • FeatureExtractExtraction of sequence and annotation, e.g. intron/exon structure, from GenBank format files
  • GibbsClusterSimultaneous alignment and clustering of peptide data
  • MHCMotifViewerEasy browsing and visualisation of MHC class I and II binding motifs.
  • MatrixPlotVisualizing structural sequence constraints.
  • MaxAlignMaximizing the size of gap-free columns by selecting an optimal subset of sequences in an alignment.
  • RedHomReduction of sequence similarity in a data set
  • RevTransMultiple alignment of coding DNA using protein level information
  • Seq2LogoSequence logo generator
  • TreeHuggerConstructing NJ or UPGMA trees from DNA and Protein alignments.
  • VirtualRibosomeA comprehensive tool for translating DNA sequences to the corresponding peptide sequences.
  • JetsetSelecting an optimal microarray probe set to represent a gene


  • AraCleanArabidopsis thaliana data set
  • CellCycleCell cycle related data sets and supplementary information
  • DNA2protSSmRNA sequences and the corresponding protein secondary structure assignments
  • DOGSDatabase Of Genome Sizes
  • GlycateBaseDatabase of glycation data for ε amino groups of lysines
  • MetaGenomic SpeciesInformation on metagenomic species (MGS)and co-abundance gene groups (CAGs) of the human gut
  • NESbaseDatabase of nuclear export signals
  • NetStartTranslation initiation site data sets
  • OglycBaseDatabase of O-glycosylated proteins
  • PhosphobaseDatabase of phosphorylation sites, has moved to EMBL
  • PlantExprSupplementary plant gene expression data for scientific publications
  • SignalP datasetsSignal peptide data sets