OrthoDB

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• • • Genes & Genomes
  • • Evolution & Phylogeny

  • • Database
  • • Software tool

  SwissOrthology

  One-stop shop for orthologs
• • • Evolution & Phylogeny

  • • Database

  OrthoDB SPARQL endpoint

  SPARQL access to the OrthoDB catalog of orthologs
• • • Evolution & Phylogeny

  • • Software tool

  OrthoLoger

  Accurate and scalable inference of groups of orthologs
• • • Evolution & Phylogeny

  • • Database
  • • Software tool

  OMA

  Orthology inference among complete genomes
• • • Evolution & Phylogeny

  • • Database

  OMA SPARQL endpoint

  SPARQL access to the OMA Orthology database
• • • Genes & Genomes
  • • Proteins & Proteomes
  • • Structural Biology

  • • Database

  ViralZone

  Factsheets about viruses linked to sequence databases
• • • Proteins & Proteomes

  • • Database

  UniProtKB/Swiss-Prot

  Protein knowledgebase
• • • Proteins & Proteomes

  • • Database

  UniProtKB

  Protein sequence database
• • • Proteins & Proteomes

  • • Software tool

  HAMAP-Scan

  Scanning of protein sequences against HAMAP families
• • • Genomics

  • • Database

  TASmania

  Toxin-antitoxin database
• • • Genomics

  • • Software tool

  TASer

  Search tool associated to TASmania
• • • Proteins & Proteomes

  • • Database

  UniProt SPARQL endpoint

  SPARQL access to UniProt and related data
• • • Proteins & Proteomes

  • • Software tool

  ScanProsite

  Protein sequences against PROSITE
• • • Systems Biology

  • • Software tool

  OMAMO

  OMAMO allows the user to find the best simple model organism
• • • Transcriptomics
  • • Evolution & Phylogeny
  • • Systems Biology

  • • Database
  • • Software tool

  SwissRegulon Portal

  Tools and data for regulatory genomics
• • • Genes & Genomes
  • • Systems Biology

  • • Software tool

  CREMA

  Cis-Regulatory Element Motif Activities
• • • Transcriptomics
  • • Systems Biology

  • • Software tool

  CRUNCH

  Automated pipeline for ChIP-seq data analysis
• • • Transcriptomics

  • • Database

  PolyAsite

  Database of curated RNA polyadenylation sites
• • • Genomics

  • • Database
  • • Software tool

  EPD

  Eukaryotic Promoter Database
• • • Transcriptomics

  • • Database
  • • Software tool

  ASAP

  Web-based, cooperative portal for single-cell data analyses
• • • Systems Biology

  • • Database

  Cellosaurus

  Knowledge resource on cell lines
• • • Systems Biology

  • • Database

  Cellosaurus SPARQL endpoint

  SPARQL access to Cellosaurus
• • • Transcriptomics
  • • Evolution biology

  • • Database
  • • Software tool

  Bgee

  Gene expression expertise
• • • Transcriptomics
  • • Evolution biology

  • • Database

  Bgee SPARQL endpoint

  SPARQL access to the Bgee gene expression database
• • • Proteins & Proteomes
  • • Systems Biology

  • • Database
  • • Software tool

  STRING

  Protein-protein interaction networks and enrichment analysis
• • • Proteins & Proteomes
  • • Structural Biology

  • • Database

  SWISS-MODEL Repository

  Protein structure homology models
• • • Proteins & Proteomes
  • • Glycomics

  • • Database

  GlyConnect

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

  • • Database

  UniLectin

  Structural and functional classification of lectins
• • • Transcriptomics
  • • Systems Biology

  • • Database

  SwissRegulon

  Database of genome-wide annotations of regulatory sites
• • • Proteins & Proteomes
  • • Glycomics

  • • Database

  MatrixDB

  Extracellular proteins and polysaccharides interactions
• • • Proteins & Proteomes

  • • Database
  • • Software tool

  PaxDb

  Protein abundance across several organisms
• • • Structural Biology

  • • Database

  ModelArchive

  Repository of predicted macromolecular structure models
• • • Transcriptomics

  • • Software tool

  miRmap

  Prediction of microRNA target repression strength
• • • Genomics
  • • Evolution biology

  • • Database

  Selectome

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

  • • Database
  • • Software tool

  MetaNetX

  Metabolic network repository & analysis
• • • Proteins & Proteomes
  • • Metabolomics

  • • Database

  MetaNetX SPARQL endpoint

  SPARQL access to MetaNetX
• • • Proteins & Proteomes

  • • Database

  ABCD

  Database of chemically defined antibodies
• • • Transcriptomics

  • • Software tool

  TagScan

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

  • • Database

  SugarBind

  Pathogen Sugar-Binding Database
• • • Genomics
  • • Population genetics

  • • Software tool

  V-pipe

  Viral genomics pipeline
• • • Genomics
  • • Population genetics

  • • Software tool

  V-pipe SARS-CoV-2

  V-pipe pipeline for SARS-CoV-2 sequencing data
• • • Genes & Genomes

  • • Database
  • • Software tool

  SPSP | Swiss Pathogen Surveillance Platform

  Public Swiss pathogen NGS data
• • • Genomics
  • • Evolution & Phylogeny

  • • Software tool

  Nextclade

  Clade assignment, mutation calling & QC for virus sequences
• • • Genes & Genomes
  • • Evolution biology

  • • Software tool

  BEAST2

  Bayesian evolutionary analysis by sampling trees
• • • Genomics
  • • Evolution biology

  • • Software tool

  GenSpectrum

  Real-time pathogen genomic sequence analysis
• • • Genomics
  • • Evolution biology

  • • Software tool

  Nextstrain

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

  • • Software tool

  BUSCO

  From QC to gene prediction and phylogenomics
• • • Metagenomics

  • • Software tool

  mVIRs

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

  • • Database

  Pathoplexus

  Human viral pathogen genomic data sharing platform
• • • Proteins & Proteomes

  • • Database
  • • Software tool

  HAMAP

  UniProtKB family classification and annotation
• • • Proteins & Proteomes

  • • Database

  HAMAP SPARQL endpoint

  SPARQL access to the HAMAP annotation rules
• • • Proteins & Proteomes
  • • Text mining & Machine learning

  • • Database
  • • Software tool

  MixTCRpred

  Predictor of TCR-epitope interactions
• • • Proteins & Proteomes

  • • Database
  • • Software tool

  neXtProt

  Human protein knowledgebase
• • • Glycomics

  • • Software tool

  HMO-Glycologue

  Simulator of Human Milk Oligosaccharide synthesis
• • • Systems Biology

  • • Software tool

  CLASTR

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

  • • Software tool

  SwissTargetPrediction

  Target prediction for bioactive small molecules
• • • Genes & Genomes
  • • Systems Biology

  • • Database

  cancercelllines.org

  Genomic variants in human cancer cell lines
• • • Genomics
  • • Systems Biology

  • • Database

  arrayMAP

  Curated array data repository for cancer genomics
• • • Genomics

  • • Database
  • • Software tool

  SNP2TFBS

  Regulatory SNPs affecting TF binding site affinity
• • • Genes & Genomes
  • • Systems Biology

  • • Database

  Progenetix

  Genomic profiles of cancer samples with focus on CNV
• • • Structural Biology
  • • Glycomics

  • • Database

  UniCarb-DB

  Glycan structures and associated mass spectrometry data
• • • Text mining & Machine learning

  • • Software tool

  Variomes

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

  • • Software tool

  raxmlGUI

  raxmlGUI 2.0 is a graphical user interface to RAxML
• • • Evolution & Phylogeny

  • • Database

  SwissTree

  A collection of gold standard gene phylogenies
• • • Evolution & Phylogeny

  • • Software tool

  Phylo.io

  A tool for visualising and comparing phylogenetic trees
• • • Genes & Genomes
  • • Evolution biology

  • • Software tool

  GenomeHistory

  Gene duplicate identification