SIB Resources

      • Proteins & Proteomes
      • Lipidomics
      • Database

    SwissLipids

    Knowledge resource for lipids
      • Proteins & Proteomes
      • Glycomics
      • Database

    Glyco@Expasy

    Zooming in on web-based glycoinformatics resources
      • Proteins & Proteomes
      • Systems Biology
      • Database
      • Software tool

    STRING

    Protein-protein interaction networks and enrichment analysis
      • Genomics
      • Population genetics
      • Software tool

    V-pipe

    Viral genomics pipeline
      • Drug design
      • , Medicinal chemistry
      • Database
      • Software tool

    SwissDrugDesign

    Widening access to computer-aided drug design
      • Genes & Genomes
      • Evolution & Phylogeny
      • Database
      • Software tool

    SwissOrthology

    One-stop shop for orthologs
      • Proteins & Proteomes
      • Structural Biology
      • Database
      • Software tool

    SWISS-MODEL

    Protein structure homology-modelling
      • Systems Biology
      • Database

    Cellosaurus

    Knowledge resource on cell lines
      • Genomics
      • Evolution biology
      • Software tool

    Nextstrain

    Impact of pathogen genome data on science and public health
      • Transcriptomics
      • Evolution biology
      • Database
      • Software tool

    Bgee

    Gene expression expertise
      • Transcriptomics
      • Software tool

    ASAP

    Web-based, cooperative portal for single-cell data analyses
      • Genes & Genomes
      • , Genomics
      • , Transcriptomics
      • Evolution & Phylogeny
      • Systems Biology
      • Database
      • Software tool

    SwissRegulon Portal

    Tools and data for regulatory genomics
      • Proteins & Proteomes
      • Systems Biology
      • , Metabolomics
      • Database

    Rhea

    Expert-curated database of biochemical reactions

Other Resources of SIB Groups

      • Transcriptomics
      • Software tool

    ISA

    Finding modules in gene expression data
      • Genomics
      • , Transcriptomics
      • Systems Biology
      • Database

    SwissRegulon

    Database of genome-wide annotations of regulatory sites
      • Proteins & Proteomes
      • Systems Biology
      • Database
      • Software tool

    MetaNetX

    Metabolic network repository & analysis
      • Genes & Genomes
      • , Genomics
      • Systems Biology
      • Database
      • Software tool

    Progenetix

    Genomic profiles of cancer samples with focus on CNV
      • Evolution & Phylogeny
      • Database
      • Software tool

    OMA

    Orthology inference among complete genomes
      • Genomics
      • , Transcriptomics
      • Software tool

    QuasR

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

    RandSeq

    Random protein sequence generator
      • Structural analysis
      • Software tool

    OpenStructure

    Molecular modelling and visualisation environment
      • Systems Biology
      • Software tool

    CLASTR

    Cellosaurus STR similarity search tool
      • Genes & Genomes
      • Evolution & Phylogeny
      • Software tool

    REALPHY

    Inference of phylogenetic trees from genome data
      • Genomics
      • Software tool

    FastEpistasis

    Tool for quantitative trait epistasis
      • Genes & Genomes
      • Systems Biology
      • Software tool

    CREMA

    Cis-Regulatory Element Motif Activities
      • Proteins & Proteomes
      • Glycomics
      • Database
      • Software tool

    GlyConnect

    Integrated data platform to study glycosylation
      • Proteins & Proteomes
      • Structural Biology
      • , Structural analysis
      • Software tool

    SWISS-MODEL Workspace

    Fully automated protein structure homology-modeling server
      • Text mining & Machine learning
      • Database
      • Software tool

    SIBiLS

    Personalized information retrieval from the literature
      • Transcriptomics
      • Evolution biology
      • Database

    Bgee SPARQL endpoint

    SPARQL access to the Bgee gene expression database
      • Proteins & Proteomes
      • Structural Biology
      • , Medicinal chemistry
      • Software tool

    SwissDock

    Docking of small ligands into protein active sites
      • Genomics
      • Software tool

    IScan

    Insertion sequence identification in whole genomes
      • Glycomics
      • Software tool

    GlyS3

    Match a glycan substructure to a database of full structures
      • Genomics
      • , Transcriptomics
      • Software tool

    TromER

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

    ScanProsite

    Protein sequences against PROSITE
      • Genomics
      • Systems Biology
      • Database
      • Software tool

    arrayMAP

    Curated array data repository for cancer genomics
      • Proteins & Proteomes
      • Medicinal chemistry
      • , Structural analysis
      • Database

    SwissBioIsostere

    Database of molecular replacements for ligand design
      • Population genetics
      • Software tool

    Arlequin

    An integrated software for population genetics data analysis
      • Genomics
      • Software tool

    MADAP

    Clustering tool of genomic sites
      • Text mining & Machine learning
      • Software tool

    Biodiversity PMC

    Search a large collection of scientific publications
      • Proteins & Proteomes
      • Software tool

    UniProt BLAST

    BLAST sequence similarity search on the UniProt web site
      • Proteins & Proteomes
      • Text mining & Machine learning
      • Database

    MHC Motif Atlas

    MHC Motif Atlas
      • Text mining & Machine learning
      • Software tool

    COVTriage

    Rank the COVID-19 literature according to COVoc ontology
      • Proteins & Proteomes
      • Metabolomics
      • Software tool

    rawrr

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

    SugarBind

    Pathogen Sugar-Binding Database
      • Evolution & Phylogeny
      • Software tool

    raxmlGUI

    raxmlGUI 2.0 is a graphical user interface to RAxML
      • Proteins & Proteomes
      • Systems Biology
      • Database

    TCS

    Predict interaction specificity in bacterial signalling
      • Genomics
      • , Transcriptomics
      • Proteins & Proteomes
      • Software tool

    Translate

    Nucleotide sequence to a protein sequence
      • Genomics
      • Software tool

    TagScan

    Genome-wide sequence tag scanner
      • Evolution & Phylogeny
      • Software tool

    Phylo.io

    A tool for visualising and comparing phylogenetic trees
      • Genomics
      • Database

    TASmania

    Toxin-antitoxin database
      • Proteins & Proteomes
      • Software tool

    Sulfinator

    Predict tyrosine sulfation sites in protein sequences
      • Genomics
      • Software tool

    TASer

    Search tool associated to TASmania
      • Proteins & Proteomes
      • Database

    neXtProt

    Human protein knowledgebase
      • Proteins & Proteomes
      • Database
      • Software tool

    MyHits

    Relationships between protein sequences and motifs
      • Systems Biology
      • Database

    SwissBioPics

    Subcellular location visualization
      • Glycomics
      • Software tool

    Glynsight

    Visualise and compare glycan expression profiles
      • Proteins & Proteomes
      • Software tool

    PRATT

    Conserved patterns in a set of protein sequences
      • Proteins & Proteomes
      • Database

    UniProtKB

    Protein sequence database
      • Genomics
      • Evolution biology
      • , Population genetics
      • Software tool

    fastsimcoal

    Fast sequential Markov coalescent simulation of genomic data
      • Proteins & Proteomes
      • Glycomics
      • Database

    UniLectin

    Structural and functional classification of lectins
      • Medicinal chemistry
      • Software tool

    SwissADME

    Pharmacokinetics properties and druglikeness
      • Genomics
      • Evolution & Phylogeny
      • Software tool

    Nextclade

    Clade assignment, mutation calling & QC for virus sequences
      • Proteins & Proteomes
      • Software tool

    Compute pI/MW

    Isoelectric point and molecular weight from protein sequence
      • Transcriptomics
      • Systems Biology
      • Software tool

    DWT-online

    Dinucleotide Weight Tensor toolbox and visualisation service
      • Evolution & Phylogeny
      • Database

    Swiss-Trees

    A collection of gold standard gene phylogenies
      • Genes & Genomes
      • Evolution biology
      • Software tool

    BEAST2

    Bayesian evolutionary analysis by sampling trees
      • Text mining & Machine learning
      • Software tool

    Variomes

    Search engine to support the curation of genomic variants
      • Evolution & Phylogeny
      • Software tool

    OrthoLoger

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

    SIM

    Alignment of two protein sequences or within a sequence
      • Genomics
      • Database

    EPD

    Eukaryotic Promoter Database
      • Proteins & Proteomes
      • Software tool

    Dotlet

    Regions of close similarity in 2 sequences
      • Proteins & Proteomes
      • Medicinal chemistry
      • , Structural analysis
      • Software tool

    SwissTargetPrediction

    Target prediction for bioactive small molecules
      • Genes & Genomes
      • Software tool

    ESTscan

    Detect coding regions in EST sequences
      • Proteins & Proteomes
      • Software tool

    Myristoylator

    N-terminal myristoylation of proteins by neural networks
      • Genomics
      • , Transcriptomics
      • Database

    Glittr

    Git repositories with bioinformatics training material
      • Transcriptomics
      • Database

    PolyAsite

    Database of curated RNA polyadenylation sites
      • Genomics
      • , Transcriptomics
      • Systems Biology
      • Software tool

    ISMARA

    Webservice for gene expression and epigenetic data analysis
      • Proteins & Proteomes
      • Systems Biology
      • , Metabolomics
      • Database

    Rhea SPARQL endpoint

    SPARQL access to the Rhea knowledgebase
      • Metagenomics
      • Software tool

    LEMMI

    Continuous benchmarking of methods for metagenomics
      • Metabolomics
      • Software tool

    MSight

    Mass Spectrometry Imager
      • Systems Biology
      • , Glycomics
      • Software tool

    HMO-Glycologue

    Simulator of Human Milk Oligosaccharide synthesis
      • Proteins & Proteomes
      • Glycomics
      • Software tool

    GlycoMod

    Possible oligosaccharide structures on proteins from masses
      • Genomics
      • , Transcriptomics
      • Software tool

    SIBsim4

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

    SNP2TFBS

    Regulatory SNPs affecting TF binding site affinity
      • Evolution biology
      • Software tool

    CAPTAIN

    Decision-support tool for conservation area prioritization
      • Evolution & Phylogeny
      • Database

    OrthoDB

    Ortholog evolutionary and functional annotations
      • Proteins & Proteomes
      • Software tool

    HAMAP-Scan

    Scanning of protein sequences against HAMAP families
      • Genomics
      • Software tool

    SSA

    Analysis of nucleic acid sequence motifs
      • Proteins & Proteomes
      • Structural Biology
      • Database
      • Software tool

    CAMEO

    Weekly automated benchmarking of protein structure modelling
      • Genomics
      • Evolution biology
      • Database

    Selectome

    Database of positive selection
      • Genomics
      • Proteins & Proteomes
      • Database

    ABCD

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

    FindMod

    Potential PTMs and single amino acid substitutions
      • Genes & Genomes
      • , Genomics
      • Systems Biology
      • Database
      • Software tool

    iPtgxDBs

    Platform for integrated proteogenomics databases
      • Genomics
      • Systems Biology
      • Software tool

    Phylogibbs

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

    FindPept

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

    MALDIPepQuant

    Quantify MALDI peptides from Phenyx output
      • Genes & Genomes
      • , Genomics
      • , Metagenomics
      • Software tool

    mVIRs

    Prediction tool for inducible, bacteria-infecting viruses
      • Proteins & Proteomes
      • Software tool

    PeptideCutter

    Potential cleavage sites in a protein
      • Genes & Genomes
      • Evolution biology
      • Software tool

    GenSpectrum

    Real-time pathogen genomic sequence analysis
      • Genomics
      • Software tool

    PACMAN

    Publication quality images of DNA locations
      • Proteins & Proteomes
      • Database

    PROSITE

    Protein family and domain database
      • Proteins & Proteomes
      • Database
      • Software tool

    HAMAP

    UniProtKB family classification and annotation
      • Text mining & Machine learning
      • Software tool

    BiotXplorer

    Biotic interactions from scientific publications
      • Glycomics
      • Software tool

    EpitopeXtractor

    Compare glycan structures to Glydin' network's collection
      • Genomics
      • , Transcriptomics
      • Evolution biology
      • Software tool

    BUSCO

    From QC to gene prediction and phylogenomics
      • Proteins & Proteomes
      • Database

    VenomZone

    Portal to venom protein UniProtKB entries
      • Genes & Genomes
      • , Genomics
      • Database
      • Software tool

    SVIP

    Clinical interpretation of variants in cancer
      • Proteins & Proteomes
      • Glycomics
      • Software tool

    MzJava

    Open source Java class library to process MS fragmentation
      • Medicinal chemistry
      • , Structural analysis
      • Software tool

    SwissParam

    Topology and parameters for small molecules
      • Genomics
      • Software tool

    ShoRAH

    Analysis of NGS data
      • Proteins & Proteomes
      • Software tool

    OMArk

    OMArk determines the quality and completeness of gene sets
      • Proteins & Proteomes
      • Glycomics
      • Software tool

    Swiss Mass Abacus

    Intuitive calculator of peptide and glycopeptide masses
      • Proteins & Proteomes
      • Database
      • Software tool

    PaxDb

    Protein abundance across several organisms
      • Proteins & Proteomes
      • Software tool

    pROC

    Visualize, smooth and compare ROC curves
      • Structural Biology
      • Database

    ModelArchive

    Repository of predicted macromolecular structure models
      • Proteins & Proteomes
      • Software tool

    ProtParam

    Computation of physico chemical parameters of a protein
      • Proteins & Proteomes
      • Database

    ENZYME

    Enzyme nomenclature database
      • Proteins & Proteomes
      • Structural analysis
      • Software tool

    QMEAN

    Protein model quality estimation
      • Glycomics
      • Software tool

    SugarSketcher

    Fast, intuitive, SNFG-compliant glycan structure drawing
      • Genomics
      • Evolution biology
      • Software tool

    CT-CBN

    Estimate conjunctive Bayesian networks
      • Genomics
      • Software tool

    ChIP-Seq

    ChIP-Seq data analysis tools
      • Proteins & Proteomes
      • Structural Biology
      • , Drug design
      • , Medicinal chemistry
      • , Structural analysis
      • Database

    Click2Drug

    Directory of computational drug design tools
      • Proteins & Proteomes
      • Software tool

    PeptideMass

    Theoretical protein cleavage by a given enzyme
      • Glycomics
      • Software tool

    GlycoDigest

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

    mOTUs

    Microbial taxonomic and population genomic profiler
      • Genes & Genomes
      • , Genomics
      • Text mining & Machine learning
      • Database

    cancercelllines.org

    Genomic variants in human cancer cell lines
      • Genomics
      • , Transcriptomics
      • Systems Biology
      • Software tool

    CRUNCH

    Automated pipeline for ChIP-seq data analysis
      • Glycomics
      • Database

    UniCarb-DB

    Glycan structures and associated mass spectrometry data
      • Transcriptomics
      • Software tool

    ExpressionView

    Biclusters identified in gene expression data
      • Genes & Genomes
      • Proteins & Proteomes
      • Structural Biology
      • Database

    ViralZone

    Fact sheets about viruses linked to sequence databases
      • Genomics
      • Population genetics
      • Software tool

    V-pipe SARS-CoV-2

    V-pipe pipeline for SARS-CoV-2 sequencing data
      • Glycomics
      • Software tool

    Glydin'

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

    MELANIE

    2-D PAGE analysis
      • Proteins & Proteomes
      • Software tool

    pftools

    Build, calibrate, and search biological sequences
      • Glycomics
      • Database

    GAG-DB

    3D structures of glycosaminoglycans
      • Proteins & Proteomes
      • Systems Biology
      • Database

    Protein Universe Atlas

    Interactive, annotated similarity network of all proteins
      • Proteins & Proteomes
      • Medicinal chemistry
      • , Structural analysis
      • Database

    SwissSidechain

    Database of non-natural amino acid side chains
      • Proteins & Proteomes
      • Glycomics
      • Software tool

    GlycoSiteAlign

    Multiple alignment of sequences around glycosylation sites
      • Proteins & Proteomes
      • Software tool

    ProtScale

    Profile produced by amino acids scales on protein sequences
      • Genomics
      • , Transcriptomics
      • Software tool

    miRmap

    Prediction of microRNA target repression strength
      • Systems Biology
      • Software tool

    OMAMO

    OMAMO allows the user to find the best simple model organism