Expasy: Swiss Bioinformatics Resource Portal
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SIB Resources

Over 160 high-quality database and software tools are provided by SIB Groups to the global life science community. They are hosted on Expasy, SIB’s bioinformatics resource portal. Among them, several key resources - the SIB Resources - benefit from the Institute’s specific support. For more info visit https://www.sib.swiss/database-software-tools/sib-resources.
      • Transcriptomics
      • Evolution biology
      • Database
      • Software tool

    Bgee
    Gene expression expertise
      • Proteins & Proteomes
      • Systems Biology
      • Database
      • Software tool

    STRING
    Protein-protein interaction networks and enrichment analysis
      • Proteins & Proteomes
      • Lipidomics
      • Database

    SwissLipids
    Knowledge resource for lipids
      • Systems Biology
      • Database

    Cellosaurus
    Knowledge resource on cell lines
      • Genomics
      • Population genetics
      • Software tool

    V-pipe
    Viral genomics pipeline
      • Genomics
      • Evolution biology
      • Software tool

    Nextstrain
    Impact of pathogen genome data on science and public health
      • Metagenomics
      • Population genetics
      • Database
      • Software tool

    mOTUs
    Microbial taxonomic and population genomic profiler
      • Proteins & Proteomes
      • Metabolomics
      • Database

    Rhea
    Expert-curated database of biochemical reactions
      • Genes & Genomes
      • Evolution & Phylogeny
      • Database
      • Software tool

    SwissOrthology
    One-stop shop for orthologs
      • Medicinal chemistry
      • Database
      • Software tool

    SwissDrugDesign
    Widening access to computer-aided drug design
      • Transcriptomics
      • Evolution & Phylogeny
      • Systems Biology
      • Database
      • Software tool

    SwissRegulon Portal
    Tools and data for regulatory genomics
      • Proteins & Proteomes
      • Structural Biology
      • Database
      • Software tool

    SWISS-MODEL
    Protein structure homology-modelling
      • Transcriptomics
      • Software tool

    ASAP
    Web-based, cooperative portal for single-cell data analyses
      • Proteins & Proteomes
      • Glycomics
      • Database

    Glyco@Expasy
    Zooming in on web-based glycoinformatics resources
      • Genes & Genomes
      • Evolution biology
      • Software tool

    BEAST2
    Bayesian evolutionary analysis by sampling trees

Other Resources of SIB Groups

      • Proteins & Proteomes
      • Database

    UniProtKB
    Protein sequence database
      • Genomics
      • Evolution biology
      • Database

    Selectome
    Database of positive selection
      • Proteins & Proteomes
      • Database

    PROSITE
    Protein family and domain database
      • Proteins & Proteomes
      • Medicinal chemistry
      • Software tool

    SwissDock
    Docking of small ligands into protein active sites
      • Proteins & Proteomes
      • Database

    ENZYME
    Enzyme nomenclature database
      • Proteins & Proteomes
      • Database
      • Software tool

    HAMAP
    UniProtKB family classification and annotation
      • Genes & Genomes
      • Proteins & Proteomes
      • Structural Biology
      • Database

    ViralZone
    Fact sheets about viruses linked to sequence databases
      • Proteins & Proteomes
      • Database

    neXtProt
    Human protein knowledgebase
      • Evolution & Phylogeny
      • Database

    OrthoDB
    Ortholog evolutionary and functional annotations
      • Evolution & Phylogeny
      • Database
      • Software tool

    OMA
    Orthology inference among complete genomes
      • Proteins & Proteomes
      • Metabolomics
      • Database
      • Software tool

    MetaNetX
    Metabolic network repository & analysis
      • Proteins & Proteomes
      • Database

    VenomZone
    Portal to venom protein UniProtKB entries
      • Population genetics
      • Software tool

    Arlequin
    An integrated software for population genetics data analysis
      • Proteins & Proteomes
      • Glycomics
      • Database

    UniLectin
    Structural and functional classification of lectins
      • Glycomics
      • Database

    UniCarb-DB
    Glycan structures and associated mass spectrometry data
      • Genomics
      • Database

    EPD
    Eukaryotic Promoter Database
      • Transcriptomics
      • Software tool

    TromER
    Prediction of transcribed regions and splice junctions
      • Proteins & Proteomes
      • Structural analysis
      • Software tool

    SwissTargetPrediction
    Target prediction for bioactive small molecules
      • Proteins & Proteomes
      • Structural analysis
      • Database

    SwissSidechain
    Database of non-natural amino acid side chains
      • Genomics
      • Software tool

    TagScan
    Genome-wide sequence tag scanner
      • Transcriptomics
      • Systems Biology
      • Database

    SwissRegulon
    Database of genome-wide annotations of regulatory sites
      • Structural analysis
      • Software tool

    SwissParam
    Topology and parameters for small molecules
      • Proteins & Proteomes
      • Structural analysis
      • Database

    SwissBioIsostere
    Database of molecular replacements for ligand design
      • Medicinal chemistry
      • Software tool

    SwissADME
    Pharmacokinetics properties and druglikeness
      • Proteins & Proteomes
      • Glycomics
      • Software tool

    Swiss Mass Abacus
    Intuitive calculator of peptide and glycopeptide masses
      • Glycomics
      • Software tool

    SugarSketcher
    Fast, intuitive, SNFG-compliant glycan structure drawing
      • Glycomics
      • Database

    SugarBind
    Pathogen Sugar-Binding Database
      • Genomics
      • Software tool

    SSA
    Analysis of nucleic acid sequence motifs
      • Genomics
      • Database
      • Software tool

    SNP2TFBS
    Regulatory SNPs affecting TF binding site affinity
      • Transcriptomics
      • Software tool

    SIBsim4
    Align expressed RNA sequences on a DNA template
      • Genomics
      • Software tool

    ShoRAH
    Analysis of NGS data
      • Genes & Genomes
      • Evolution & Phylogeny
      • Software tool

    REALPHY
    Inference of phylogenetic trees from genome data
      • Transcriptomics
      • Software tool

    QuasR
    Quantification and analysis of Short Reads
      • Proteins & Proteomes
      • Structural analysis
      • Software tool

    QMEAN
    Protein model quality estimation
      • Genomics
      • Systems Biology
      • Database
      • Software tool

    Progenetix
    Genomic profiles of cancer samples with focus on CNV
      • Proteins & Proteomes
      • Software tool

    pftools
    Build, calibrate, and search biological sequences
      • Proteins & Proteomes
      • Database
      • Software tool

    PaxDb
    Protein abundance across several organisms
      • Genomics
      • Software tool

    PACMAN
    Publication quality images of DNA locations
      • Structural analysis
      • Software tool

    OpenStructure
    Molecular modelling and visualisation environment
      • Genomics
      • Systems Biology
      • Database
      • Software tool

    arrayMAP
    Curated array data repository for cancer genomics
      • Proteins & Proteomes
      • Software tool

    MSight
    Mass Spectrometry Imager
      • Transcriptomics
      • Software tool

    miRmap
    Prediction of microRNA target repression strength
      • Genomics
      • Software tool

    MADAP
    Clustering tool of genomic sites
      • Genomics
      • Software tool

    IScan
    Insertion sequence identification in whole genomes
      • Genomics
      • Systems Biology
      • Database
      • Software tool

    iPtgxDBs
    Platform for integrated proteogenomics databases
      • Proteins & Proteomes
      • Software tool

    MELANIE
    2-D PAGE analysis
      • Glycomics
      • Software tool

    Glynsight
    Visualise and compare glycan expression profiles
      • Glycomics
      • Software tool

    Glydin'
    Network representation of known glycan determinants
      • Proteins & Proteomes
      • Glycomics
      • Software tool

    GlycoSiteAlign
    Multiple alignment of sequences around glycosylation sites
      • Proteins & Proteomes
      • Glycomics
      • Database

    GlyConnect
    Integrated data platform to study glycosylation
      • Glycomics
      • Software tool

    GlycoDigest
    In silico digestion of glycans by exoglycosidases
      • Genomics
      • Population genetics
      • Software tool

    fastsimcoal
    Fast sequential Markov coalescent simulation of genomic data
      • Genomics
      • Software tool

    FastEpistasis
    Tool for quantitative trait epistasis
      • Genes & Genomes
      • Software tool

    ESTscan
    Detect coding regions in EST sequences
      • Transcriptomics
      • Evolution biology
      • Software tool

    BUSCO
    From QC to gene prediction and phylogenomics
      • Transcriptomics
      • Proteins & Proteomes
      • Software tool

    Translate
    Convert a nucleotide sequence to a protein sequence
      • Proteins & Proteomes
      • Software tool

    Sulfinator
    Predict tyrosine sulfation sites in protein sequences
      • Proteins & Proteomes
      • Software tool

    SIM
    Alignment of two protein sequences or within a sequence
      • Proteins & Proteomes
      • Software tool

    RandSeq
    Random protein sequence generator
      • Proteins & Proteomes
      • Software tool

    ProtScale
    Profile produced by amino acids scales on protein sequences
      • Genomics
      • Proteins & Proteomes
      • Database

    ABCD
    Database of chemically defined antibodies
      • Proteins & Proteomes
      • Software tool

    ProtParam
    Computation of physico chemical parameters of a protein
      • Proteins & Proteomes
      • Software tool

    PRATT
    Conserved patterns in a set of protein sequences
      • Proteins & Proteomes
      • Software tool

    PeptideMass
    Theoretical protein cleavage by a given enzyme
      • Proteins & Proteomes
      • Software tool

    PeptideCutter
    Potential cleavage sites in a protein
      • Proteins & Proteomes
      • Software tool

    Myristoylator
    N-terminal myristoylation of proteins by neural networks
      • Proteins & Proteomes
      • Software tool

    MALDIPepQuant
    Quantify MALDI peptides from Phenyx output
      • Proteins & Proteomes
      • Software tool

    HAMAP-Scan
    Scanning of protein sequences against HAMAP families
      • Proteins & Proteomes
      • Glycomics
      • Software tool

    GlycoMod
    Possible oligosaccharide structures on proteins from masses
      • Proteins & Proteomes
      • Software tool

    FindPept
    Unspecific protein cleavage from experimental masses
      • Proteins & Proteomes
      • Software tool

    FindMod
    Potential PTMs and single amino acid substitutions
      • Proteins & Proteomes
      • Software tool

    Compute pI/MW
    Isoelectric point and molecular weight from protein sequence
      • Proteins & Proteomes
      • Software tool

    UniProt BLAST
    BLAST sequence similarity search on the UniProt web site
      • Genomics
      • Software tool

    ChIP-Seq
    ChIP-Seq data analysis tools
      • Proteins & Proteomes
      • Structural analysis
      • Database

    Click2Drug
    Directory of computational drug design tools
      • Transcriptomics
      • Systems Biology
      • Software tool

    CRUNCH
    Automated pipeline for ChIP-seq data analysis
      • Proteins & Proteomes
      • Software tool

    Dotlet
    Regions of close similarity in 2 sequences
      • Systems Biology
      • Software tool

    CLASTR
    Cellosaurus STR similarity search tool
      • Proteins & Proteomes
      • Structural analysis
      • Software tool

    SWISS-MODEL Workspace
    Fully automated protein structure homology-modeling server
      • Proteins & Proteomes
      • Systems Biology
      • Database

    TCS
    Predict interaction specificity in bacterial signalling
      • Genomics
      • Evolution biology
      • Software tool

    CT-CBN
    Estimate conjunctive Bayesian networks
      • Transcriptomics
      • Software tool

    ISA
    Finding modules in gene expression data
      • Transcriptomics
      • Software tool

    ExpressionView
    Biclusters identified in gene expression data
      • Transcriptomics
      • Systems Biology
      • Software tool

    ISMARA
    Webservice for gene expression and epigenetic data analysis
      • Genomics
      • Systems Biology
      • Software tool

    Phylogibbs
    Regulatory sites in a collection of DNA sequences
      • Proteins & Proteomes
      • Software tool

    pROC
    Visualize, smooth and compare ROC curves
      • Proteins & Proteomes
      • Software tool

    ScanProsite
    Protein sequences against PROSITE
      • Genomics
      • Population genetics
      • Software tool

    V-pipe SARS-CoV-2
    V-pipe pipeline for SARS-CoV-2 sequencing data
      • Text mining & Machine learning
      • Software tool

    COVTriage
    Rank the COVID-19 literature according to COVoc ontology
      • Genomics
      • Database

    TASmania
    Toxin-antitoxin database
      • Genomics
      • Software tool

    TASer
    Search tool associated to TASmania
      • Transcriptomics
      • Evolution biology
      • Database

    Bgee SPARQL endpoint
    SPARQL access to the Bgee gene expression database
      • Metagenomics
      • Software tool

    LEMMI
    Continuous benchmarking of methods for metagenomics
      • Evolution & Phylogeny
      • Software tool

    OrthoLoger
    Accurate and scalable inference of groups of orthologs
      • Proteins & Proteomes
      • Metabolomics
      • Software tool

    rawrr
    R package for fast reading Thermo Fisher Scientific MS data
      • Transcriptomics
      • Database

    PolyAsite
    Database of curated RNA polyadenylation sites
      • Text mining & Machine learning
      • Database
      • Software tool

    SIBiLS
    Personalized information retrieval from the literature
      • Evolution & Phylogeny
      • Software tool

    raxmlGUI
    raxmlGUI 2.0 is a graphical user interface to RAxML
      • Glycomics
      • Software tool

    HMO-Glycologue
    Simulator of Human Milk Oligosaccharide synthesis
      • Text mining & Machine learning
      • Software tool

    Variomes
    Search engine to support the curation of genomic variants
      • Metagenomics
      • Software tool

    mVIRs
    Prediction tool for inducible, bacteria-infecting viruses
      • Systems Biology
      • Software tool

    OMAMO
    OMAMO allows the user to find the best simple model organism
      • Evolution & Phylogeny
      • Software tool

    Phylo.io
    A tool for visualising and comparing phylogenetic trees
      • Evolution & Phylogeny
      • Database

    Swiss-Trees
    A collection of gold standard gene phylogenies
      • Genomics
      • Evolution & Phylogeny
      • Software tool

    Nextclade
    Clade assignment, mutation calling & QC for virus sequences
      • Systems Biology
      • Database

    SwissBioPics
    Subcellular location visualization
      • Proteins & Proteomes
      • Text mining & Machine learning
      • Database

    MHC Motif Atlas
    MHC Motif Atlas
      • Structural Biology
      • Database

    ModelArchive
    Repository of predicted macromolecular structure models
      • Proteins & Proteomes
      • Structural Biology
      • Database
      • Software tool

    CAMEO
    Weekly automated benchmarking of protein structure modelling
      • Evolution biology
      • Software tool

    CAPTAIN
    Decision-support tool for conservation area prioritization
      • Transcriptomics
      • Database

    Glittr
    Git repositories with bioinformatics training material
      • Genomics
      • Text mining & Machine learning
      • Database

    cancercelllines.org
    Genomic variants in human cancer cell lines
      • Genes & Genomes
      • Systems Biology
      • Software tool

    CREMA
    Cis-Regulatory Element Motif Activities
      • Transcriptomics
      • Systems Biology
      • Software tool

    DWT-online
    Dinucleotide Weight Tensor toolbox and visualisation service
      • Genomics
      • Evolution biology
      • Software tool

    GenSpectrum
    Real-time pathogen genomic sequence analysis
      • Proteins & Proteomes
      • Systems Biology
      • Database

    Protein Universe Atlas
    Interactive, annotated similarity network of all proteins
      • Proteins & Proteomes
      • Software tool

    OMArk
    OMArk determines the quality and completeness of gene sets
      • Text mining & Machine learning
      • Software tool

    BiotXplorer
    Biotic interactions from scientific publications
      • Text mining & Machine learning
      • Software tool

    Biodiversity PMC
    Search a large collection of scientific publications
      • Proteins & Proteomes
      • Database

    EnzChemRED
    Enzyme Chemistry Relation Extraction Dataset
      • Glycomics
      • Software tool

    GlycoQL
    Match a glycan substructure to a database of full structures
      • Genomics
      • Database

    Pathoplexus
    Human viral pathogen genomic data sharing platform
      • Transcriptomics
      • Systems Biology
      • Software tool

    Cellstates
    Infering clusters of cells in scRNA-seq data
      • Transcriptomics
      • Systems Biology
      • Software tool

    Sanity
    Single-cell RNA-Seq normalization method
      • Proteins & Proteomes
      • Glycomics
      • Database

    MatrixDB
    Extracellular proteins and polysaccharides interactions
      • Proteins & Proteomes
      • Software tool

    prolfqua
    R package for protein differential expression analysis