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
- 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
- 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
- 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 alleles 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
- 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
Enzyme Activity class prediction
- CAZyPPrediction of Glycoside Hydrolase Activity and Substrate Specificity
- AMUSERDesigning optimal primers for USER fusion.
- BioReaderBiomedical Research Article Distiller
- 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 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