• • • Systems Biology

  • • Database
  • • Software tool

  Cellosaurus

  Knowledge resource on cell lines
• • • Proteins & Proteomes

  • • Database

  neXtProt

  Human protein knowledgebase
• • • Proteins & Proteomes
  • • Systems Biology

  • • Database

  Rhea

  Expert-curated database of biochemical reactions.
• • • Evolution biology

  • • Software tool

  Nextstrain

  Impact of pathogen genome data on science and public health
• • • Genes & Genomes
    • , Genomics
    • , Transcriptomics
  • • Evolution biology

  • • Database
  • • Software tool

  Bgee

  Gene expression expertise
• • • Genomics
    • , 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.
• • • Proteins & Proteomes

  • • Database

  SwissLipids

  Knowledge resource for lipids
• • • Genomics

  • • Database

  EPD

  Eukaryotic Promoter Database
• • • Genes & Genomes

  • • Database
  • • Software tool

  SwissRegulon Portal

  Tools and data for regulatory genomics
• • • Proteins & Proteomes

  • • Database

  STRING

  Protein-protein interaction networks and enrichment analysis
• • • Transcriptomics
  • • Population genetics

  • • Software tool

  V-pipe

  Viral genomics pipeline
• • • Proteins & Proteomes

  • • Database

  UniProtKB/Swiss-Prot

  Protein knowledgebase
• • • Genes & Genomes
  • • Evolution biology

  • • Database
  • • Software tool

  SwissOrthology

  One-stop shop for orthologs
• • • Proteins & Proteomes

  • • Database
  • • Software tool

  SWISS-MODEL

  Protein structure homology-modelling
• • • Drug design

  • • Software tool

  SwissDrugDesign

  Widening access to computer-aided drug design

Other Resources of SIB Groups

• • • Genomics

  • • Software tool

  PACMAN

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

  • • Software tool

  MzJava

  Open source Java class library to process MS fragmentation
• • • Glycomics

  • • Database

  UniCarb-DB

  Glycan structures and associated mass spectrometry data
• • • Genomics
    • , Metagenomics
    • , Transcriptomics
  • • Population genetics

  • • Software tool

  mOTUs

  Microbial taxonomic and population genomic profiler
• • • Proteins & Proteomes

  • • Database

  STRING-covid

  New COVID-19 oriented version of the STRING database
• • • Genomics
  • • Evolution biology

  • • Software tool

  BUSCO

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

  • • Software tool

  rawrr

  R package for fast reading Thermo Fisher Scientific MS data.
• • • Proteins & Proteomes

  • • Software tool

  FindPept

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

  • • Database

  World-2DPAGE Repository

  Repository for published gel-based proteomics data
• • • Proteins & Proteomes

  • • Database

  PROSITE

  Protein family and domain database
• • • Population genetics

  • • Software tool

  Arlequin

  An integrated software for population genetics data analysis
• • • Proteins & Proteomes
  • • Evolution biology

  • • Software tool

  RAxML

  Inference of large phylogenetic trees
• • • Genomics

  • • Software tool

  SSA

  Analysis of nucleic acid sequence motifs
• • • Proteins & Proteomes

  • • Software tool

  pftools

  Build, calibrate, and search biological sequences
• • • Evolution & Phylogeny

  • • Database

  miROrtho

  Catalogue of animal microRNA genes
• • • Genomics
  • • Evolution biology

  • • Database
  • • Software tool

  CEGA

  Conserved Elements from Genomic Alignments
• • • Proteins & Proteomes
  • • Systems Biology

  • • Database
  • • Software tool

  MetaNetX

  Metabolic network repository & analysis
• • • Genomics
    • , Transcriptomics

  • • Software tool

  miRmap

  Prediction of microRNA target repression strength
• • • Genomics

  • • Software tool

  TASer

  Search tool associated to TASmania
• • • Proteins & Proteomes

  • • Software tool

  MALDIPepQuant

  Quantify MALDI peptides from Phenyx output
• • • Genes & Genomes
  • • Proteins & Proteomes
  • • Evolution & Phylogeny
    • , Evolution biology

  • • Software tool

  OrthoLoger

  Accurate and scalable inference of groups of orthologs
• • • Systems Biology

  • • Software tool

  Genome History

  Gene duplicate identification
• • • Evolution biology

  • • Software tool

  REALPHY

  Inference of phylogenetic trees from genome data
• • • Evolution & Phylogeny

  • • Database
  • • Software tool

  OMA

  Orthology inference among complete genomes
• • • Transcriptomics
  • • Population genetics

  • • Software tool

  V-pipe SARS-CoV-2

  V-pipe pipeline applied to SARS-CoV-2 sequencing data
• • • Genomics

  • • Software tool

  ShoRAH

  Analysis of NGS data
• • • Proteins & Proteomes
  • • Systems Biology

  • • Database

  Rhea SPARQL endpoint

  SPARQL access to the Rhea DB
• • • Proteins & Proteomes

  • • Database

  HAMAP SPARQL endpoint

  Use HAMAP + SPARQL to generate portable annotation pipelines
• • • Genes & Genomes
  • • Population genetics

  • • Software tool

  COVID-19 Scenarios

  Public health planning tool for COVID-19 outbreaks
• • • Structural analysis

  • • Software tool

  rBAN

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

  • • Software tool

  MELANIE

  2-D PAGE analysis
• • • Evolution & Phylogeny

  • • Database
  • • Software tool

  OMA SPARQL endpoint

  Orthology inference among complete genomes
• • • Transcriptomics

  • • Database

  PolyAsite

  Database of curated RNA polyadenylation sites
• • • Proteins & Proteomes

  • • Software tool

  UniProt ClustalO

  Align two or more protein sequences
• • • Genes & Genomes
    • , Genomics
    • , Metagenomics

  • • Software tool

  mVIRs

  Prediction tool for inducible, bacteria-infecting viruses
• • • Transcriptomics

  • • Software tool

  ISA

  Finding modules in gene expression data
• • • Proteins & Proteomes
  • • Structural Biology

  • • Database

  SWISS-MODEL Repository

  Protein structure homology models
• • • Evolution biology

  • • Database

  Selectome

  Database of positive selection
• • • Proteins & Proteomes

  • • Software tool

  FindMod

  Potential PTMs and single amino acid substitutions
• • • Genomics
    • , Transcriptomics

  • • Software tool

  ESTscan

  Detect coding regions in EST sequences
• • • Glycomics

  • • Software tool

  GlyS3

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

  • • Database

  ENZYME

  Enzyme nomenclature database
• • • Proteins & Proteomes

  • • Software tool

  BLAST

  BLAST sequence similarity search
• • • Glycomics

  • • Database

  SugarBind

  Pathogen Sugar-Binding Database
• • • Genomics
  • • Systems Biology

  • • Database
  • • Software tool

  Progenetix

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

  • • Database

  OrthoDB

  Ortholog evolutionary and functional annotations
• • • Genomics
  • • Systems Biology

  • • Database
  • • Software tool

  arrayMAP

  Curated array data repository for cancer genomics
• • • Text mining & Machine learning

  • • Software tool

  Computational Linguistics for COVID-19

  Central hub in computational linguistics for COVID-19
• • • Genomics
  • • Systems Biology

  • • Software tool

  Phylogibbs

  Regulatory sites in a collection of DNA sequences
• • • Glycomics

  • • Database

  GAG-DB

  3D structures of glycosaminoglycans
• • • Proteins & Proteomes

  • • Software tool

  Compute pI/MW

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

  • • Software tool

  GlycoMod

  Possible oligosaccharide structures on proteins from masses
• • • Glycomics

  • • Software tool

  PepSweetener

  Human intact N-glycopeptide mass matching tool
• • • Genomics

  • • Software tool

  ZFN-Site

  Search zinc finger nuclease target and off-target sites
• • • Glycomics

  • • Software tool

  HMO-Glycologue

  Simulator of Human Milk Oligosaccharide synthesis
• • • Proteins & Proteomes

  • • Database
  • • Software tool

  MyHits

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

  • • Software tool

  QMEAN

  Protein model quality estimation
• • • Genomics
  • • Evolution biology

  • • Database

  ImmunoDB

  Insect immune-related genes and gene families
• • • Genomics
    • , Transcriptomics

  • • Software tool

  QuasR

  Quantification and analysis of Short Reads
• • • Genes & Genomes
    • , Genomics
  • • Systems Biology

  • • Database
  • • Software tool

  iPtgxDBs

  Platform for integrated proteogenomics databases
• • • Proteins & Proteomes

  • • Database

  ViralZone

  Fact sheets about viruses; linked to sequence databases.
• • • Glycomics

  • • Software tool

  GlyConnect Compozitor

  Contextualises glycan composition sets
• • • Proteins & Proteomes

  • • Database
  • • Software tool

  HAMAP

  UniProtKB family classification and annotation
• • • Genes & Genomes
  • • Evolution & Phylogeny

  • • Software tool

  BEAST2 - COVID-19 Monitoring

  Epidemiological dynamics in real-time
• • • Proteins & Proteomes

  • • Software tool

  Decrease redundancy

  Redundancy reduction in a set of sequences
• • • Proteins & Proteomes

  • • Database

  PaxDb

  Protein abundance across several organisms
• • • Evolution & Phylogeny

  • • Software tool

  raxmlGUI

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

  • • Software tool

  GlycoDigest

  In silico digestion of glycans by exoglycosidases
• • • Genomics

  • • Software tool

  MADAP

  Clustering tool of genomic sites
• • • Proteins & Proteomes
  • • Medicinal chemistry
    • , Structural analysis

  • • Software tool

  SwissTargetPrediction

  Target prediction for bioactive small molecules
• • • Glycomics

  • • Software tool

  Glydin'

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

  • • Software tool

  SwissDock

  Docking of small ligands into protein active sites
• • • Proteins & Proteomes
  • • Structural analysis

  • • Software tool

  OpenStructure

  Molecular modelling and visualisation environment
• • • Proteins & Proteomes
  • • Glycomics

  • • Software tool

  Swiss Mass Abacus

  Intuitive calculator of peptide and glycopeptide masses
• • • Evolution biology
    • , Population genetics

  • • Software tool

  CT-CBN

  Estimate conjunctive Bayesian networks
• • • Genomics

  • • Software tool

  FastEpistasis

  Tool for quantitative trait epistasis
• • • Proteins & Proteomes

  • • Software tool

  SIM

  Alignment of two protein sequences or within a sequence
• • • Proteins & Proteomes
  • • Systems Biology

  • • Software tool

  Biochemical Pathways

  Roche Biochemical Pathways
• • • Population genetics
  • • Systems Biology

  • • Software tool

  CRUNCH

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

  • • Database

  ABCD

  Database of chemically defined antibodies
• • • Medicinal chemistry

  • • Software tool

  SwissSimilarity

  Ligand-based virtual screening
• • • Glycomics

  • • Software tool

  EpitopeXtractor

  Compare glycan structures to Glydin' network's collection
• • • Proteins & Proteomes

  • • Software tool

  neXtProt SPARQL endpoint

  SPARQL endpoint for the neXtProt Human protein knowledgebase
• • • Proteins & Proteomes
  • • Structural analysis

  • • Software tool

  MARCOIL

  Coiled-coil regions in protein sequences
• • • Proteins & Proteomes

  • • Software tool

  RandSeq

  Random protein sequence generator
• • • Genomics
    • , Transcriptomics

  • • Software tool

  tromer

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

  • • Software tool

  PeptideMass

  Theoretical protein cleavage by a given enzyme
• • • Proteins & Proteomes

  • • Software tool

  Make2D-DB II

  Build web-based proteomics databases
• • • Genomics

  • • Database

  OpenFlu

  Database for human and animal influenza virus
• • • Proteins & Proteomes

  • • Software tool

  HAMAP-Scan

  Scanning of protein sequences against HAMAP families
• • • Genomics

  • • Software tool

  ChIP-Seq

  ChIP-Seq data analysis tools
• • • Genomics

  • • Database
  • • Software tool

  SNP2TFBS

  Regulatory SNPs affecting TF binding site affinity
• • • Proteins & Proteomes
  • • Medicinal chemistry
    • , Structural analysis

  • • Software tool

  SwissParam

  Topology and parameters for small molecules
• • • Glycomics

  • • Software tool

  Glycoforest

  Partial de novo glycan sequencing method based on MS/MS data
• • • Genomics

  • • Software tool

  MAMOT

  Hidden Markov modelling Tool
• • • Proteins & Proteomes
  • • Structural Biology
    • , Medicinal chemistry
    • , Structural analysis

  • • Software tool

  Click2Drug

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

  • • Software tool

  MSight

  Mass Spectrometry Imager
• • • Proteins & Proteomes

  • • Software tool

  ScanProsite

  Protein sequences against PROSITE
• • • Proteins & Proteomes

  • • Software tool

  Sulfinator

  Predict tyrosine sulfation sites in protein sequences
• • • Genomics

  • • Software tool

  TagScan

  Genome-wide sequence tag scanner
• • • Proteins & Proteomes

  • • Software tool

  Myristoylator

  N-terminal myristoylation of proteins by neural networks.
• • • Proteins & Proteomes

  • • Software tool

  PeptideCutter

  Potential cleavage sites in a protein
• • • Genomics
  • • Evolution & Phylogeny

  • • Database

  Corona OMA Browser

  The OMA Browser, for 119 Nidovirales species
• • • Medicinal chemistry
    • , Structural analysis

  • • Database

  SwissSidechain

  Database of non-natural amino acid side chains
• • • Genes & Genomes
    • , Genomics
    • , Transcriptomics
  • • Evolution biology

  • • Database
  • • Software tool

  Bgee SPARQL endpoint

  Gene expression expertise
• • • Proteins & Proteomes
  • • Medicinal chemistry
    • , Structural analysis

  • • Database

  SwissBioIsostere

  Database of molecular replacements for ligand design
• • • Genes & Genomes

  • • Database
  • • Software tool

  SPSP | Swiss Pathogen Surveillance Platform

  A secure NGS One-health online platform
• • • Proteins & Proteomes

  • • Software tool

  PRATT

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

  • • Database

  UniLectin

  Structural and functional classification of lectins
• • • Proteins & Proteomes

  • • Software tool

  pROC

  Visualize, smooth and compare ROC curves
• • • Proteins & Proteomes
  • • Systems Biology

  • • Database

  TCS

  Predict interaction specificity in bacterial signalling
• • • Proteins & Proteomes

  • • Software tool

  UniProt BLAST

  BLAST sequence similarity search on the UniProt web site
• • • Genomics
    • , Transcriptomics
  • • Systems Biology

  • • Database

  SwissRegulon

  Database of genome-wide annotations of regulatory sites
• • • Genomics

  • • Software tool

  IScan

  Insertion sequence identification in whole genomes
• • • Proteins & Proteomes

  • • Software tool

  Dotlet

  Regions of close similarity in 2 sequences
• • • Glycomics

  • • Software tool

  Glynsight

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

  • • Software tool

  ProtScale

  Profile produced by amino acids scales on protein sequences
• • • Proteins & Proteomes
  • • Glycomics

  • • Database
  • • Software tool

  GlyConnect

  Integrated data platform to study glycosylation
• • • Proteins & Proteomes

  • • Database

  UniProt SPARQL endpoint

  Query UniProt + related data in a powerful SQL-like language
• • • Genomics
  • • Evolution & Phylogeny

  • • Software tool

  Newick Utilities

  High-throughput phylogenetic tree processing
• • • Text mining & Machine learning

  • • Software tool

  Variomes

  Search engine to support the curation of genomic variants
• • • Proteins & Proteomes
  • • Glycomics

  • • Software tool

  GlycoSiteAlign

  Multiple alignment of sequences around glycosylation sites
• • • Genomics

  • • Database

  TASmania

  Toxin-antitoxin database
• • • Genomics
    • , Transcriptomics
  • • Proteins & Proteomes
  • • Systems Biology

  • • Software tool

  ISMARA

  Genome-wide annotations of regulatory sites
• • • Proteins & Proteomes
  • • Medicinal chemistry

  • • Software tool

  SwissADME

  Pharmacokinetics properties and druglikeness
• • • Systems Biology

  • • Software tool

  CLASTR

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

  • • Software tool

  Swiss-PdbViewer

  Display, analyse and superimpose protein 3D structures
• • • Genes & Genomes
    • , Genomics

  • • Database
  • • Software tool

  SVIP

  Clinical interpretation of variants in cancer
• • • Genomics

  • • Software tool

  LEMMI

  Continuous benchmarking of methods for metagenomics
• • • Proteins & Proteomes
  • • Structural Biology
    • , Structural analysis

  • • Software tool

  SWISS-MODEL Workspace

  Fully automated protein structure homology-modeling server
• • • Genomics
  • • Proteins & Proteomes

  • • Software tool

  SIB COVID-19 Integrated Knowledgebase

  Integrated data relevant for research on SARS-CoV-2
• • • Genomics
  • • Evolution biology
    • , Population genetics

  • • Software tool

  fastsimcoal

  Fast sequential Markov coalescent simulation of genomic data
• • • Transcriptomics

  • • Software tool

  ExpressionView

  Biclusters identified in gene expression data
• • • Glycomics

  • • Software tool

  SugarSketcher

  Fast, intuitive, SNFG-compliant glycan structure drawing
• • • Genomics
    • , Transcriptomics

  • • Software tool

  SIBsim4

  Align expressed RNA sequences on a DNA template
• • • Proteins & Proteomes

  • • Database

  VenomZone

  Portal to venom protein UniProtKB entries
• • • Evolution & Phylogeny

  • • Database

  OrthoDB SPARQL endpoint

  Evolutionary and functional annotations of orthologs
• • • Proteins & Proteomes

  • • Database

  UniProtKB

  Protein sequence database
• • • Proteins & Proteomes

  • • Software tool

  ProtParam

  Computation of physico chemical parameters of a protein
• • • Text mining & Machine learning

  • • Database
  • • Software tool

  SIBiLS

  Personalized Information Retrieval in biomedical literature
• • • Genomics
    • , Transcriptomics
  • • Proteins & Proteomes

  • • Software tool

  Translate

  Nucleotide sequence to a protein sequence
• • • Text mining & Machine learning

  • • Software tool

  CovidTriage

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

  • • Software tool

  FetchGWI / tagger

  Short sequence mapping
• • • Proteins & Proteomes

  • • Database

  COVID-19 UniProtKB

  UniProtKB data for COVID-19 / SARS-CoV-2 research.