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Alphabetical Index
SIB resources
External resources - (No support from the ExPASy Team)
a
- AACompIdent • protein identification by aa composition
- AACompSim • amino acid composition comparison
- Agadir • Prediction of the helical content of peptides
- ALF • simulation of genome evolution
- Alignment tools • Four tools for multiple alignments
- AllAll • protein sequences comparisons
- Anolea • Atomic Non-Local Environment Assessment
- APSSP • Advanced Protein Secondary Structure Prediction
- Arlequin • software for population genetics
- Ascalaph • Molecular modeling software
- Association Viewer • SNPs display in a genetic context
b
- BayeScan • identify natural selection
- Bgee • gene expression patterns comparison
- big-PI • predict GPI modification sites
- Biochemical Pathways • Biochemical Pathways
- BIONJ • Neighbor Joining (NJ) phylogenetic analysis
- BLAST • sequence similarity search
- BLAST (UniProt) • BLAST search on the UniProt web site
- BLAST - NCBI • Biological sequence similarity search
- BLAST - PBIL • BLAST search on protein sequence databases
- Blast2Fasta • Blast to Fasta conversion
- BLASTO • BLAST on orthologous groups
- boxshade • MSA pretty printer
c
- CFSSP • Protein secondary structure prediction
- ChIP-Seq • ChIP-Seq data analysis tools
- ChloroP • chloroplast transit peptides & cleavage sites
- Click2Drug • Directory of computational drug design tools
- CLIPZ • binding sites of RNA-binding proteins
- ClustalO (UniProt) • Align two or more protein sequences
- ClustalW • Multiple sequence alignment
- ClustalW - PBIL • Multiple sequence alignment program
- ClustalW2 • Multiple sequence alignment program
- Codon Suite • codon-based sequence analysis
- Coiled-Coils prediction • Prediction of coiled coils regions
- COILS • Prediction of Coiled Coil Regions in Proteins
- ColorSeq • Color Protein Sequence
- Compute pI/MW • theoretical pI and Mw computation
- CPHmodels • Protein homology modeling
- CSS-Palm • Prediction of palmitoylation sites in proteins
- CT-CBN • estimate conjunctive Bayesian networks
d
- DAS-TMfilter • Prediction of transmembrane regions
- Decrease redundancy • Sequence redundancy reduction
- DendroUPGMA • Dendrogram creation using the UPGMA algorithm
- DIALIGN • Local multiple sequence aligment
- DictyOGlyc • GlcNAc O-glycosylation sites in D.discoideum
- DisEMBL • Prediction of disordered protein regions
- DLP-SVM • Domain linker predictor
- Dotlet • sequence similarity plots
e
- EasyProt • graphical platform for proteomics analysis
- efmtool • elementary flux modes of metabolic networks
- ELM • Eukaryotic Linear Motifs
- ElMMo • miRNA target predictions
- EMBnet services • bioinformatics tools, databases and courses
- EMBOSS translation tools • sequence translation tools
- ENZYME • enzyme nomenclature
- EPD • collection of eukaryotic promoters
- epestfind • Identification of PEST motifs
- ESTscan • coding region detection
- ESyPred3D • Protein homology modeling
- Evolutionary Trace Server (TraceSuite II) • Maps evolutionary traces to structures
- ExpressionView • explore biclusters in gene expression data
f
- FASTA/SSEARCH/GGSEARCH/GLSEARCH • Sequence similarity searching of protein db
- FastEpistasis • test for epistasis effects
- fastsimcoal • coalescent simulation of genomic data
- FetchGWI / tagger • short sequence mapping
- FindMod • protein post-translational modification prediction
- FindPept • peptide identification from unspecific cleavage
- FingerPRINTScan • scan sequences against PRINTS
- FUGUE • Sequence-structure homology recognition
g
- GENIO/logo • RNA/DNA & Amino Acid Sequence Logos
- Geno3D • Protein molecular modelling
- Genome History • duplicate genes from complete genomes
- GlobPlot • Protein disorder/globularity/domain predictor
- GlycanMass • oligosaccharide structure mass calculation
- GlycoMod • oligosaccharide structure prediction
- GlycoSuiteDB • glycan database
- Glycoviewer • visualize a set of glycan structures
- GMM • copy number variation detection
- GOR • Protein secondary structure prediction
- GPI-SOM • identify GPI-anchor signals
- GPS • Prediction of kinase-specific phosphorylation site
- GPSDB • gene and protein synonyms
- Graphical Codon Usage Analyser • Codon bias
h
- HAMAP • UniProtKB family classification and annotation
- HamapScan • Scan protein sequences against the HAMAP families
- HCA (hydrophobic cluster analysis) • hydrophobic cluster analysis
- HCD/CID spectra merger • combine HCD and CID MS/MS spectra
- HeliQuest • alpha-helical properties screening
- HHpred • Homology detection & structure prediction
- HMMTOP • Prediction of transmembranes helices and topology
- HTMSRAP • Helical TransMembrane Prediction
i
- ImageMaster / Melanie • software for 2-D PAGE analysis
- ImmunoDB • insect immune-related genes and gene families
- InterProScan • Family and domain datatabase search
- ISA • gene expression module discovery
- IScan • insertion sequence identification
- ISMARA • genome-wide expression data modeling
- IsotopIdent • theoretical isotopic distribution
j
k
- Kalign - EBI • Fast and accurate multiple sequence alignment
- Kalign - SBC • Fast and accurate multiple sequence alignment
l
- LALIGN • Pairwise alignment
- Linear Classification • simple linear classification
- LipoP • predict lipoproteins and signal peptides
- LiveBench • Continuous Benchmarking of Structure Prediction Se
m
- MADAP • clustering for genome annotation data
- MAFFT - CBRC • Multiple sequence aligment
- MAFFT - EBI • Multiple sequence aligment
- Make2D-DB II • package to build web-based proteomics database
- MakeMultimer.py • Reconstruction of multimeric molecules in crystals
- MALDIPepQuant • quantify MALDI peptides
- MAMOT • HMM models
- MARCOIL • coiled-coils prediction
- MarvinSpace • Visualization, modeling and interactive rendering
- Mascot • protein identification from mass spectrometry data
- MassSearch • sequence search by mass spectrometry weights
- MaxAlign • Gap removal from alignments
- Medline Ranker • Ranking the biomedical literature
- MeDor • Metaserver for protein disorder prediction
- MetaNetX • Metabolic Network Repository & Analysis
- MIAPEGelDB • MIAPE document edition
- miROrtho • catalogue of animal microRNA genes
- MITOPROT • predict mitochondrial targeting sequences
- MLtree • maximum likelihood optimization
- MLTreeMap • phylogenetics and functionalities of metagenomes
- MolTalk • Environment for structural bioinformatics
- MovieMaker • Generates movies of protein dynamics
- MSight • mass spectrometry imager
- Multialin • Multiple sequence alignment
- Multicoil • Prediction of two- and three-stranded coiled coils
- MUSCLE • Multiple alignment server
- MyDomains • Image Creator
- MyHits • protein domains database and tools
- Myristoylator • N-terminal myristoylation prediction
n
- NetAcet • predict N-terminal acetylation sites
- NetCGlyc • C-mannosylation sites in mammalian proteins
- NetCorona • Coronavirus 3C-like proteinase cleavage sites
- NetGlycate • glycation of epsilon amino groups of lysines
- NetNES • Prediction of leucine-rich nuclear export signals
- NetNGlyc • N-glycosylation sites in human proteins
- NetOGlyc • mammalian mucin type GalNAc O-glycosylation sites
- NetPhos • predict phosphorylation in eukaryotes
- NetPhosK • Prediction of kinase-specific phosphorylation site
- NetPhosYeast • predict protein phosphorylation sites in yeast
- NetPicoRNA • Prediction of picornaviral protease cleavage sites
- NetSurfP • Protein Surface Accessibility Prediction
- NetTurnP • Prediction of Beta-turn regions in proteins
- Newick Utilities • high-throughput phylogenetic tree processing
- neXtProt • human proteins
- nfswatch • monitoring NFS traffic
- NMT • Predict N-terminal N-myristoylation of proteins
- NQ-Flipper • Correction of unfavorable rotamers of Asn and Gln
o
- OMA • orthology inference among complete genomes.
- OMSSA • MS/MS identification tool
- One to Three • 1- to 3-letter amino acid converter
- OpenFlu • Influenza genetic and epidemiological data
- OpenStructure • molecular modelling and visualization
- OrthoDB • Hierarchical catalog of eukaryotic orthologs
p
- Paircoil • Prediction of coiled coils regions
- Paircoil2 • Prediction of coiled coils regions
- PANDITplus • protein families and domains resources
- PATS • predict apicoplast targeted sequences
- PattInProt • scan sequences against patterns, mismatch allowed
- PaxDb • protein abundance database
- PDBePISA • Protein Interfaces, Surfaces and Assemblies
- PepDraw • Peptide primary structure drawing
- PepFrag • Identify proteins from a tandem mass spectrum
- PepMapper • Peptide mass fingerprinting tool
- PepPepSearch • sequence-based search of Swiss-Prot
- Peptide Builder • Builds simple peptides and proteins
- PeptideCutter • protein cleavage sites prediction
- PeptideMass • peptides from protein cleavage
- PEPVAC • Prediction of MHCI-restricted epitopes
- Pfam HMM Search • Pfam database search
- pftools • Generalized profiles build and search tools
- Phobius • predict transmembrane topology and signal peptides
- PHYLIP • Package of programs for phyologenetic analysis
- Phylogenetic Tree • phylogenetic tree construction and printing
- Phylogeny programs • Links to phylogeny programs
- Phylogeny.fr • Simple phylogenetic analysis
- Phylogibbs • regulatory sites discovery
- Phyre2 • 3D structure prediction with HMM
- pIcarver • theoretical distributions of peptide pI
- Ping pong algorithm • coherent patterns across paired datasets
- PLOGO • Sequence logos
- Poodle • Prediction of disordered protein regions
- PoPMuSiC • Thermodynamic stability prediction upon mutations
- PORTER • Protein Secondary Structure Prediction
- PPSearch • search a sequence against PROSITE patterns
- PRATT • find patterns in unaligned protein sequences
- PRATT (EBI) • find conserved patterns in unaligned sequences
- PredictProtein • Prediction of physico-chemical protein properties
- Predotar • predict putative N-terminal targeting sequences
- PrePS • predict protein prenylation
- pROC • visualize, smooth and compare ROC curves
- PROCHECK • Stereochemical quality of a protein structure
- ProDom • Scan a sequence against ProDom domain families
- PROF • Secondary Structure Prediction System
- ProFound • Search protein databases with peptide mass maps
- Prolune • Popular science articles (in French)
- ProP • Prediction of Arg & Lys propeptide cleavage sites
- PROPSEARCH • Functional and / or structural homolog search
- ProSA-web • Program of error recognition in 3D structures
- PROSITE • protein domains and families
- ProtBud • Comparison of asymmetric units and biological unit
- Protein Colourer • Tool for colouring amino acid sequences
- Protein Disorder Predictors • Protein Disorder Predictors
- Protein Model Portal • structural information for a protein
- Protein Sequence Logos • Protein sequence logo method
- Protein Spotlight • Informally written reviews on proteins
- ProteinProspector • Mass spectrometry database search tools
- ProtParam • protein physical and chemical parameters
- ProtScale • protein profile computation and representation
- PSIPRED • Various protein structure prediction methods
- PSORT • Protein subcellular location prediction
- PTS1 • peroxisomal targeting signal 1 containing proteins
- PVS - Protein Variability Server • Protein sequence variability in MSA
- PyMOL • Molecular graphics visualization
q
r
- Radar • De novo repeat detection in protein sequences
- RandSeq • random protein sequence generator
- Rankpep • Prediction of MHC type I and II peptide binding
- RasMol • Molecular graphics visualization
- RAxML • ML inference of large phylogenetic trees
- REP • Protein search for repeats
- REPRO • De novo repeat detection in protein sequences
- Reverse Transcription and Translation Tool • Transcription, translation, reverse transcription
- Reverse Translate • Reverse translation
s
- SAM-T08 • HMM-based Protein Structure Prediction
- SAMBA • Systolic Accelerator for Molecular Biological Appl
- SAPS • Statistical analysis of protein sequences
- ScanProsite • scan protein sequence(s) against PROSITE
- Scratch Protein Predictor • protein structure & structural features prediction
- SecretomeP • Prediction of non-classical protein secretion
- Selectome • positive selection
- Seq2Logo • Protein sequence logo method
- SeqLogos • Sequence logo from amino acid alignment
- Sequence Similarity Maps (SSM) • data mining of viral isolates
- Sequence Variability Server • Protein sequence variability in MSA
- Sequerome • BLAST similarity search and sequence profiling
- SHOPS • Genomic operon context analysis
- ShoRAH • tools for the analysis of NGS data
- SIBsim4 • spliced sequence alignment
- SignalP • Prediction of signal peptide cleavage sites
- SIM • binary sequence alignment
- SMART • genetically mobile domains and domain architecture
- SmileMS • LC-MSMS software for small molecule identification
- smirnaDB • miRNA expression profiles analysis
- Soaplab services • web services interface to bioinformatics tools
- SOPMA • Secondary structure prediction.
- SOSUI • Classification and Secondary Structure Prediction
- SSA • nucleic acid sequence motifs
- Strap • Structural alignments of proteins
- STRING • protein-protein interactions
- SugarBind • pathogen sugar-binding
- Sulfinator • tyrosine sulfation site prediction
- SulfoSite • Prediction of tyrosine sulfations sites
- SUMOplot • Prediction of sumoylation sites in proteins
- SUMOsp • Prediction of sumoylation sites
- Superfamily Sequence search • Search Sequences for SCOP domains
- SUPERFAMILY Sequence Search • Assign SCOP domains to sequence using SUPERFAMILY
- SuperTree • assemble phylogenetic trees
- SWISS-2DPAGE • proteins on 2-D and SDS PAGE maps
- SWISS-MODEL Repository • protein structure homology models
- SWISS-MODEL Workspace • structure homology-modeling
- Swiss-PdbViewer • analyse protein 3D structures
- SwissBioIsostere • bioIsosteres for small molecules
- SwissDock • protein ligand docking server
- SwissParam • topology, parameters for small organic molecules
- SwissRegulon • annotations of regulatory sites
- SwissSidechain • non-natural amino-acid sidechains
- SwissVar • variants in UniProtKB entries
- SYFPEITHI • Prediction of MHC type I and II peptide binding
t
- T-Coffee • sequence and structure multiple alignments
- T-Coffee - EBI • Multiple sequence alignment program
- T-Coffee - WUR • Multiple sequence alignment program
- T-REKS • De novo repeat detection in protein sequences
- TagIdent • protein identification with PI, Mw and tag
- TagScan • genome-wide sequence tag scanner
- TargetP • Subcellular location prediction
- TatP • Twin-arginine signal peptides prediction
- TCS • interaction specificity in two-component systems
- TEIRESIAS • discover patterns in nucleic or aminoacid sequence
- TermiNator • Prediction of N-terminal modification
- The Miner Suite • Tools for data analysis
- The PhylOgenetic Web Repeater (POWER) • Phylogenetic analysis
- The Systems Biology Research Tool • software and API for systems biologists
- Three to One • 3- to 1-letter amino acid converter
- Three- / one-letter code • 3- to 1-letter amino acid converter and inversely
- TLS Motion Determination • Translation/Libration/Screw Motion Determination
- TMHMM • Prediction of transmembrane helices in proteins
- TMPred • membrane-spanning region prediction
- TopMatch • Protein structure comparison
- TopPred • Topology prediction of membrane proteins
- TopSearch • Gateway to protein structures
- Translate • nucleotide sequence translation
- TreeGen • phylogenetic tree from distance matrix
- TriFLe • TRFLP species identification and simulation
- tromer • transcriptome analyser
- TRUST • De novo repeat detection in protein sequences
u
- UniMES (UniProt metagenomic samples) • UniProt Metagenomic and Environmental Sequences
- UniParc (UniProt sequence archive) • UniProt sequence archive
- UniPathway • metabolic pathways for the UniProtKB
- UniProtKB • functional information on proteins
- UniProtKB/Swiss-Prot • protein sequence database
- UniRef (UniProt sequence clusters) • UniProtKB sequence clusters
v
- Vertex Cover • resolves a vertex cover problem
- ViralZone • portal to viral UniProtKB entries
- Vital-IT • life science informatics initiative
- VMD - Visual Molecular Dynamics • Molecular visualization program
w
- WebLogo • Sequence logos
- WHAT IF • Molecular modelling package
- Wise2 • Genomic sequence to protein sequence compariso
- World-2DPAGE Constellation • set of 2DPAGE resources
- World-2DPAGE Repository • gel-based proteomics data
- WU BLAST • Sequence similarity search in protein databases
x
- xComb • compute all possible crosslinks between proteins
- XplorMed • Relationship search in MEDLINE abstracts
- xQuest • search cross-linked peptides from complex samples
- XSTREAM • De novo tandem repeat detection
y
- YASARA • Molecular graphics, modeling, simulations
- YinOYang • O-beta-GlcNAc attachment sites in eukaryotes
z
- ZFN-Site • zinc finger nuclease (off-)target sites search