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Services

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
• 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

Miscellaneous

• 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

Datasets

• 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