SIB Resources

      • Proteins & Proteomes
      • Database

    neXtProt

    Human protein knowledgebase
      • Genes & Genomes
      • , Genomics
      • , Transcriptomics
      • Evolution biology
      • Database
      • Software tool

    Bgee

    Gene expression expertise
      • Proteins & Proteomes
      • Database

    SwissLipids

    Knowledge resource for lipids
      • Transcriptomics
      • Population genetics
      • Software tool

    V-pipe

    Viral genomics pipeline
      • Genomics
      • Database

    EPD

    Eukaryotic Promoter Database
      • Proteins & Proteomes
      • Database

    STRING

    Protein-protein interaction networks and enrichment analysis
      • Drug design
      • Software tool

    SwissDrugDesign

    Widening access to computer-aided drug design
      • Proteins & Proteomes
      • Database
      • Software tool

    SWISS-MODEL

    Protein structure homology-modelling
      • Genes & Genomes
      • Evolution biology
      • Database
      • Software tool

    SwissOrthology

    One-stop shop for orthologs

Other Resources of SIB Groups

      • Evolution & Phylogeny
      • Database
      • Software tool

    OMA

    Orthology inference among complete genomes
      • Proteins & Proteomes
      • Software tool

    pftools

    Build, calibrate, and search biological sequences
      • Proteins & Proteomes
      • Glycomics
      • Database

    UniLectin

    Structural and functional classification of lectins
      • Genomics
      • , Transcriptomics
      • Systems Biology
      • Database

    SwissRegulon

    Database of genome-wide annotations of regulatory sites
      • Proteins & Proteomes
      • Medicinal chemistry
      • , Structural analysis
      • Software tool

    SwissParam

    Topology and parameters for small molecules
      • Proteins & Proteomes
      • Structural Biology
      • , Structural analysis
      • Software tool

    SWISS-MODEL Workspace

    Fully automated protein structure homology-modeling server
      • Genes & Genomes
      • Proteins & Proteomes
      • Evolution & Phylogeny
      • , Evolution biology
      • Software tool

    OrthoLoger

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

    MELANIE

    2-D PAGE analysis
      • Genomics
      • Software tool

    TASer

    Search tool associated to TASmania
      • Glycomics
      • Software tool

    GlyS3

    Match a glycan substructure to a database of full structures
      • Proteins & Proteomes
      • Software tool

    UniProt BLAST

    BLAST sequence similarity search on the UniProt web site
      • Genomics
      • , Transcriptomics
      • Proteins & Proteomes
      • Software tool

    Translate

    Nucleotide sequence to a protein sequence
      • Genomics
      • Evolution biology
      • Software tool

    BUSCO

    From QC to gene prediction and phylogenomics
      • Genomics
      • , Transcriptomics
      • Proteins & Proteomes
      • Systems Biology
      • Software tool

    ISMARA

    Genome-wide annotations of regulatory sites
      • Proteins & Proteomes
      • Structural analysis
      • Software tool

    QMEAN

    Protein model quality estimation
      • Proteins & Proteomes
      • Database

    UniProtKB

    Protein sequence database
      • Proteins & Proteomes
      • Systems Biology
      • Database

    Rhea

    Expert-curated database of biochemical reactions.
      • Proteins & Proteomes
      • Evolution biology
      • Software tool

    RAxML

    Inference of large phylogenetic trees
      • Proteins & Proteomes
      • Software tool

    MALDIPepQuant

    Quantify MALDI peptides from Phenyx output
      • Genomics
      • Database

    TASmania

    Toxin-antitoxin database
      • Genomics
      • Software tool

    TagScan

    Genome-wide sequence tag scanner
      • Genomics
      • Software tool

    PACMAN

    Publication quality images of DNA locations
      • Proteins & Proteomes
      • Structural analysis
      • Software tool

    Swiss-PdbViewer

    Display, analyse and superimpose protein 3D structures
      • Transcriptomics
      • Database

    PolyAsite

    Database of curated RNA polyadenylation sites
      • Proteins & Proteomes
      • Medicinal chemistry
      • Software tool

    SwissADME

    Pharmacokinetics properties and druglikeness
      • Proteins & Proteomes
      • Software tool

    PeptideMass

    Theoretical protein cleavage by a given enzyme
      • Evolution biology
      • Software tool

    Nextstrain

    Impact of pathogen genome data on science and public health
      • Proteins & Proteomes
      • Database
      • Software tool

    EMBnet services

    The Bioinformatics toolkit
      • Genomics
      • Proteins & Proteomes
      • Evolution biology
      • Software tool

    ALF

    Simulation of genome evolution
      • Proteins & Proteomes
      • Glycomics
      • Database
      • Software tool

    GlyConnect

    Integrated data platform to study glycosylation
      • Evolution & Phylogeny
      • Database

    OrthoDB

    Ortholog evolutionary and functional annotations
      • Genomics
      • Software tool

    MADAP

    Clustering tool of genomic sites
      • Genomics
      • , Metagenomics
      • , Transcriptomics
      • Population genetics
      • Software tool

    mOTUs

    Microbial abundance and population genomic profiler
      • Glycomics
      • Software tool

    Glynsight

    Visualise and compare glycan expression profiles
      • Genomics
      • , Transcriptomics
      • Software tool

    miRmap

    Prediction of microRNA target repression strength
      • Glycomics
      • Database

    SugarBind

    Pathogen Sugar-Binding Database
      • Proteins & Proteomes
      • Structural analysis
      • Software tool

    MARCOIL

    Coiled-coil regions in protein sequences
      • Evolution biology
      • Database

    Selectome

    Database of positive selection
      • Systems Biology
      • Software tool

    CLASTR

    Cellosaurus STR similarity search tool
      • Proteins & Proteomes
      • Software tool

    Make2D-DB II

    Build web-based proteomics databases
      • Proteins & Proteomes
      • Structural analysis
      • Software tool

    OpenStructure

    Molecular modelling and visualisation environment
      • Genomics
      • , Transcriptomics
      • Software tool

    ESTscan

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

    Myristoylator

    N-terminal myristoylation of proteins by neural networks.
      • Proteins & Proteomes
      • Systems Biology
      • Database
      • Software tool

    MetaNetX

    Metabolic network repository & analysis
      • Glycomics
      • Database

    UniCarb-DB

    Glycan structures and associated mass spectrometry data
      • Genomics
      • Evolution biology
      • , Population genetics
      • Software tool

    fastsimcoal

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

    Phylogibbs

    Regulatory sites in a collection of DNA sequences
      • Genomics
      • Software tool

    SSA

    Analysis of nucleic acid sequence motifs
      • Population genetics
      • Systems Biology
      • Software tool

    CRUNCH

    Automated pipe-line for ChIP-seq data analysis
      • Proteins & Proteomes
      • Database

    ViralZone

    Fact sheets about viruses; linked to sequence databases.
      • Proteins & Proteomes
      • Software tool

    FindMod

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

    pIcarver

    Theoretical distributions of peptide pI on a given pH range
      • Proteins & Proteomes
      • Software tool

    Sulfinator

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

    tromer

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

    PRATT

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

    PeptideCutter

    Potential cleavage sites in a protein
      • Proteins & Proteomes
      • Database

    PROSITE

    Protein family and domain database
      • Genomics
      • Proteins & Proteomes
      • Structural analysis
      • Software tool

    COILS

    Prediction of coiled coil regions in proteins
      • Proteins & Proteomes
      • Database

    VenomZone

    Portal to venom protein UniProtKB entries
      • Genomics
      • Proteins & Proteomes
      • Software tool

    ClustalW

    Multiple sequence alignment
      • Proteins & Proteomes
      • Database
      • Software tool

    HAMAP

    UniProtKB family classification and annotation
      • Proteins & Proteomes
      • Metabolomics
      • Software tool

    rawR

    R package for fast reading Thermo Fisher Scientific MS data.
      • Genomics
      • , Transcriptomics
      • Software tool

    QuasR

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

    Compute pI/MW

    Isoelectric point and molecular weight from protein sequence
      • Proteins & Proteomes
      • Glycomics
      • Software tool

    Swiss Mass Abacus

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

    ProtParam

    Computation of physico chemical parameters of a protein
      • Medicinal chemistry
      • , Structural analysis
      • Database

    SwissSidechain

    Database of non-natural amino acid side chains
      • Evolution & Phylogeny
      • Database
      • Software tool

    OMA SPARQL endpoint

    Orthology inference among complete genomes
      • Evolution biology
      • Software tool

    REALPHY

    Inference of phylogenetic trees from genome data
      • Proteins & Proteomes
      • Database

    MIAPEGelDB

    Database of MIAPE documents
      • Genomics
      • Software tool

    MAMOT

    Hidden Markov modelling Tool
      • Proteins & Proteomes
      • Software tool

    SIM

    Alignment of two protein sequences or within a sequence
      • Genomics
      • Systems Biology
      • Database
      • Software tool

    Progenetix

    Genomic profiles of cancer samples with focus on CNV
      • Genomics
      • Software tool

    ZFN-Site

    Search zinc finger nuclease target and off-target sites
      • Genomics
      • Software tool

    LEMMI

    Continuous benchmarking of methods for metagenomics
      • Genes & Genomes
      • Population genetics
      • Software tool

    COVID-19 Scenarios

    Public health planning tool for COVID-19 outbreaks
      • Genomics
      • Software tool

    FastEpistasis

    Tool for quantitative trait epistasis
      • Proteins & Proteomes
      • Glycomics
      • Software tool

    GlycoMod

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

    ASAP

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

    PaxDb

    Protein abundance across several organisms
      • Glycomics
      • Software tool

    EpitopeXtractor

    Compare glycan structures to Glydin' network's collection
      • Proteins & Proteomes
      • Structural Biology
      • , Medicinal chemistry
      • Software tool

    SwissDock

    Docking of small ligands into protein active sites
      • Proteins & Proteomes
      • Medicinal chemistry
      • , Structural analysis
      • Software tool

    SwissTargetPrediction

    Target prediction for bioactive small molecules
      • Proteins & Proteomes
      • Glycomics
      • Software tool

    GlycoSiteAlign

    Multiple alignment of sequences around glycosylation sites
      • Glycomics
      • Software tool

    GlycoDigest

    In silico digestion of glycans by exoglycosidases
      • Genomics
      • Database
      • Software tool

    SNP2TFBS

    Regulatory SNPs affecting TF binding site affinity
      • Genomics
      • Proteins & Proteomes
      • Database

    ABCD

    Database of chemically defined antibodies
      • Glycomics
      • Software tool

    Glydin'

    Network representation of known glycan determinants
      • Proteins & Proteomes
      • Medicinal chemistry
      • , Structural analysis
      • Database

    SwissBioIsostere

    Database of molecular replacements for ligand design
      • Genomics
      • Database

    OpenFlu

    Database for human and animal influenza virus
      • Genomics
      • Software tool

    ChIP-Seq

    ChIP-Seq data analysis tools
      • Genomics
      • Evolution biology
      • Database

    ImmunoDB

    Insect immune-related genes and gene families
      • Genomics
      • Evolution & Phylogeny
      • Database

    Corona OMA Browser

    The OMA Browser, for 119 Nidovirales species
      • Transcriptomics
      • Population genetics
      • Software tool

    V-pipe SARS-CoV-2

    V-pipe pipeline applied to SARS-CoV-2 sequencing data
      • Structural analysis
      • Software tool

    rBAN

    Mapping of non-ribosomal peptides in SMILES format
      • Proteins & Proteomes
      • Software tool

    BLAST

    BLAST sequence similarity search
      • Transcriptomics
      • Software tool

    ExpressionView

    Biclusters identified in gene expression data
      • Proteins & Proteomes
      • Database

    COVID-19 UniProtKB

    UniProtKB data for COVID-19 / SARS-CoV-2 research.
      • Genomics
      • Proteins & Proteomes
      • Software tool

    LALIGN

    Multiple matching subsegments in two sequences
      • Proteins & Proteomes
      • Software tool

    Dotlet

    Regions of close similarity in 2 sequences
      • Proteins & Proteomes
      • Software tool

    ProtScale

    Profile produced by amino acids scales on protein sequences
      • Genomics
      • Systems Biology
      • Database
      • Software tool

    arrayMAP

    Curated array data repository for cancer genomics
      • Proteins & Proteomes
      • Database

    SWISS-2DPAGE

    Proteins on 2-D and SDS PAGE maps
      • Genomics
      • Software tool

    IScan

    Insertion sequence identification in whole genomes
      • Glycomics
      • Software tool

    SugarSketcher

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

    CEGA

    Conserved Elements from Genomic Alignments
      • Genes & Genomes
      • , Genomics
      • , Transcriptomics
      • Evolution biology
      • Database
      • Software tool

    Bgee SPARQL endpoint

    Gene expression expertise
      • Genes & Genomes
      • , Genomics
      • Systems Biology
      • Database
      • Software tool

    iPtgxDBs

    Platform for integrated proteogenomics databases
      • Proteins & Proteomes
      • Database

    ENZYME

    Enzyme nomenclature database
      • Transcriptomics
      • Software tool

    ISA

    Finding modules in gene expression data
      • Evolution & Phylogeny
      • Database

    miROrtho

    Catalogue of animal microRNA genes
      • Evolution biology
      • , Population genetics
      • Software tool

    CT-CBN

    Estimate conjunctive Bayesian networks
      • Proteins & Proteomes
      • Systems Biology
      • Database

    TCS

    Predict interaction specificity in bacterial signalling
      • Text mining & Machine learning
      • Software tool

    CovidTriage

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

    HAMAP-Scan

    Scanning of protein sequences against HAMAP families
      • Genomics
      • Evolution & Phylogeny
      • Software tool

    Newick Utilities

    High-throughput phylogenetic tree processing
      • Proteins & Proteomes
      • Software tool

    pROC

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

    MyHits

    Relationships between protein sequences and motifs
      • Proteins & Proteomes
      • Structural analysis
      • Software tool

    TMPred

    Prediction of trans-membrane regions in protein sequences
      • Proteins & Proteomes
      • Database

    STRING-covid

    New COVID-19 oriented version of the STRING database
      • Genomics
      • Proteins & Proteomes
      • Software tool

    boxshade

    MSA pretty printer
      • Proteins & Proteomes
      • Software tool

    ScanProsite

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

    Cellosaurus

    Knowledge resource on cell lines
      • Proteins & Proteomes
      • Software tool

    FindPept

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

    MSight

    Mass Spectrometry Imager
      • Genomics
      • Software tool

    ShoRAH

    Analysis of NGS data
      • Population genetics
      • Software tool

    Arlequin

    An integrated software for population genetics data analysis
      • Proteins & Proteomes
      • Software tool

    RandSeq

    Random protein sequence generator
      • Proteins & Proteomes
      • Structural Biology
      • , Medicinal chemistry
      • , Structural analysis
      • Software tool

    Click2Drug

    Directory of computational drug design tools
      • Genomics
      • , Transcriptomics
      • Software tool

    SIBsim4

    Align expressed RNA sequences on a DNA template