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Service Software Downloads

Gene finding and splice sites

EasyGeneGene finding in prokaryotes
- Version 1.2c
HMMgenePrediction of vertebrate and C. elegans genes
- Version 1.1
NetGene2Intron splice sites in human, C. elegans and A. thaliana DNA
- Version 2.42
NetStartPrediction of Translation Initiation Sites in Eukaryotes
- Version 1.0c
PromoterTranscription start sites in vertebrate DNA
- Version 2.0
RNAmmerPrediction of ribosomal RNA sub units
- Version 1.2

Immunological features

LYRALymphocyte receptor automated modelling
- Version 1.0
TCRpMHCmodelsStructural modeling tool of TCR-pMHC class I and class II complexes
- Version 1.0
VDJSolverAnalysis of human immunoglobulin VDJ recombination
- Version 1.0b
BepiPredPrediction of potential B-cell epitopes from protein sequence
- Version 3.0b
- Version 2.0c
- Version 1.0c
DiscoTopeImproved B-cell epitope prediction using AlphaFold2 modeling and inverse folding latent representations
- Version 3.0
- Version 1.1a
ICERFIREICORE-based prediction of neo-epitope immunogenicity.
- Version 1.0a
MAIT MatchCalculate similarity between CDR3 sequences and a reference database of MAIT sequences
- Version 1.0
MHCMotifDeconMotif deconvolution of Multi-allele immunopetidomics data
- Version 1.2b
- Version 1.2a
- Version 1.0a
NetAllergenProtein allergenicity prediction
- Version 1.0
NetBoLApanPrediction of peptide interactions with bovine MHC class I (BoLA) molecules.
- Version 1.0a
NetCTLPredection of CTL epitopes in protein sequences
- Version 1.2b
- Version 1.2a
NetCTLpanPan-specific integrated class I antigen presentation
- Version 1.1b
NetH2panPrediction of peptide interactions with murine MHC class I (H2) molecules.
- Version 1.0a
NetMHCNetMHC: Binding of peptides to MHC class I molecules
- Version 4.0a
- Version 3.4a
- Version 3.0c
NetMHCIIBinding of peptides to MHC class II molecules
- Version 2.3
- Version 2.2
NetMHCIIpanPan-specific binding of peptides to MHC class II mocules of known sequence
- Version 4.3i
- Version 4.2c
- Version 4.1a
- Version 4.0
- Version 3.2
- Version 3.1a
- Version 3.0c
- Version 2.0b
NetMHCconsBinding of peptides to any known MHC class I molecule
- Version 1.1a
NetMHCpanPan-specific binding of peptides to MHC class I alleles of known sequence
- Version 4.1b
- Version 4.0a
- Version 3.0a
- Version 2.8a
- Version 2.8
- Version 2.4a
NetMHCpanExpPan-specific binding of peptides to MHC class I proteins of known sequence including antigen expression
- Version 1.0
NetMHCphosPanPan-specific binding of phosphorylated peptides to HLA class I molecules.
- Version 1.0a
NetMHCstabStability of peptide:MHC-I complexes
- Version 1.0a
NetMHCstabpanPan-specific stability of peptide:MHC-I complexes
- Version 1.0cstatic
- Version 1.0b
- Version 1.0a
NetTepiT-cell epitopes restricted to prevalent HLA-A and HLA-B molecules
- Version 1.0
NetChopProteasomal cleavages (MHC ligands)
- Version 3.1d
NNAlignIdentifying sequence motifs in quantitative peptide data
- Version 2.1a
PickPocketBinding of peptides to any known MHC class I molecule using binding pocket matrix extrapolation
- Version 1.1a

Post-translational modifications of proteins

NetCGlycC-mannosylation sites in mammalian proteins
- Version 1.0c
NetNGlycN-linked glycosylation sites in human proteins
- Version 1.0d
- Version 1.0d
NetOGlycO-GalNAc (mucin type) glycosylation sites in mammalian proteins
- Version 4.0
- Version 3.1e
NetPhosGeneric phosphorylation sites in eukaryotic proteins
- Version 3.1
NetPhospanPrediction of phosphorylation using convolutional neural networks (CNNs).
- Version 1.0
ProPArginine and lysine propeptide cleavage sites in eukaryotic protein sequences
- Version 1.0c
YinOYangO-(beta)-GlcNAc glycosylation and Yin-Yang sites (intracellular/nuclear proteins)
- Version 1.2

Protein function and structure

CofactoryIdentification of Rossmann folds and prediction of FAD, NAD and NADP specificity
- Version 1.0
NetSurfPProtein secondary structure and relative solvent accessibility
- Version 3.0
- Version 2.0
- Version 1.0d
NetTurnPAmino acid predection in β-turns and β-turn types in proteins
- Version 1.0a
SigniSiteIdentification of residue-level genotype-phenotype correlations in protein multiple sequence alignments
- Version 2.1.1
TMHMMPrediction of transmembrane helices in proteins
- Version 2.0c

Protein sorting

ChloroPChloroplast transit peptides and their cleavage sites in plant proteins
- Version 1.1
DeepLocPrediction of eukaryotic protein subcellular localization using deep learning
- Version 2.1
- Version 2.0
- Version 1.0
LipoPSignal peptidase I & II cleavage sites in gram- bacteria
- Version 1.0a
MsrescueA Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments
- Version 1.1a
NetNESLeucine-rich nuclear export signals (NES) in eukaryotic proteins
- Version 1.1
SecretomePPrediction of non-classical protein secretion
- Version 1.0h
SignalPSignal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences
- Version 6.0h
- Version 5.0b
- Version 4.1g
- Version 3.0
- Version 2.0
TargetPSubcellular location of proteins: mitochondrial, chloroplastic, secretory pathway, or other
- Version 2.0
- Version 1.1b
TatPPresence and location of Twin-arginine signal peptides
- Version 1.0b

Miscellaneous

OligoWizDesign of oligonucleotides for DNA microarrays
- Version 2.0
ProtPartsProtein clustering and partitioning
- Version 1.0b

Bioinformatic Tool Software Downloads

GibbsClusterSimultaneous alignment and clustering of peptide data
- Version 2.0f
- Version 1.1b
Seq2LogoSequence logo generator
- Version 2.2
- Version 2.1
- Version 2.0

Dataset Downloads

NetStartTranslation initiation site data sets
- Version 1.0c