SIB Swiss Institute of Bioinformatics | Expasy

• • • Proteins & Proteomes
  • • Glycomics

  • • Database

  Glyco@Expasy

  Zooming in on web-based glycoinformatics resources

• • • Genomics
  • • Population genetics

  • • Software tool

  V-pipe

  Viral genomics pipeline

• • • Genes & Genomes
  • • Evolution biology

  • • Software tool

  BEAST2

  Bayesian evolutionary analysis by sampling trees

• • • Genes & Genomes
  • • Evolution & Phylogeny

  • • Database
  • • Software tool

  SwissOrthology

  One-stop shop for orthologs

• • • Transcriptomics

  • • Software tool

  ASAP

  Web-based, cooperative portal for single-cell data analyses

• • • Transcriptomics
  • • Evolution biology

  • • Database
  • • Software tool

  Bgee

  Gene expression expertise

• • • Genes & Genomes

  • • Database
  • • Software tool

  SPSP | Swiss Pathogen Surveillance Platform

  Public Swiss pathogen NGS data

• • • Proteins & Proteomes
  • • Structural Biology

  • • Database
  • • Software tool

  SWISS-MODEL

  Protein structure homology-modelling

• • • Metagenomics
  • • Population genetics

  • • Database
  • • Software tool

  mOTUs

  Microbial taxonomic and population genomic profiler

• • • Proteins & Proteomes

  • • Database

  UniProtKB/Swiss-Prot

  Protein knowledgebase

• • • Systems Biology

  • • Database

  Cellosaurus

  Knowledge resource on cell lines

• • • Proteins & Proteomes
  • • Lipidomics

  • • Database

  SwissLipids

  Knowledge resource for lipids

• • • Proteins & Proteomes
  • • Systems Biology
    • , Metabolomics

  • • Database

  Rhea

  Expert-curated database of biochemical reactions

• • • Proteins & Proteomes
  • • Systems Biology

  • • Database
  • • Software tool

  STRING

  Protein-protein interaction networks and enrichment analysis

• • • Genomics
  • • Evolution biology

  • • Software tool

  Nextstrain

  Impact of pathogen genome data on science and public health

• • • Drug design
    • , Medicinal chemistry

  • • Database
  • • Software tool

  SwissDrugDesign

  Widening access to computer-aided drug design

• • • Genes & Genomes
    • , Genomics
    • , Transcriptomics
  • • Evolution & Phylogeny
  • • Systems Biology

  • • Database
  • • Software tool

  SwissRegulon Portal

  Tools and data for regulatory genomics

Other Resources of SIB Groups

• • • Text mining & Machine learning

  • • Software tool

  Computational Linguistics for COVID-19

  Central hub in computational linguistics for COVID-19

• • • Proteins & Proteomes
  • • Glycomics

  • • Database

  GlyConnect SPARQL endpoint

  SPARQL access to GlyConnect

• • • Genes & Genomes
  • • Proteins & Proteomes
  • • Structural Biology

  • • Database

  ViralZone

  Fact sheets about viruses linked to sequence databases

• • • Proteins & Proteomes
  • • Glycomics

  • • Software tool

  GlycoSiteAlign

  Multiple alignment of sequences around glycosylation sites

• • • Proteins & Proteomes
  • • Metabolomics

  • • Database

  MetaNetX SPARQL endpoint

  SPARQL access to MetaNetX

• • • Proteins & Proteomes

  • • Database

  neXtProt

  Human protein knowledgebase

• • • Proteins & Proteomes

  • • Software tool

  OMArk

  OMArk determines the quality and completeness of gene sets

• • • Proteins & Proteomes

  • • Software tool

  Dotlet

  Regions of close similarity in 2 sequences

• • • Glycomics

  • • Database

  UniCarb-DB

  Glycan structures and associated mass spectrometry data

• • • Proteins & Proteomes

  • • Database

  HAMAP SPARQL endpoint

  SPARQL access to the HAMAP annotation rules

• • • Text mining & Machine learning

  • • Database

  SIBiLS SPARQL endpoint

  SPARQL access to SIBiLS, the SIB Literature Services

• • • Genomics
    • , Transcriptomics
  • • Systems Biology

  • • Software tool

  CRUNCH

  Automated pipeline for ChIP-seq data analysis

• • • Proteins & Proteomes

  • • Database

  ENZYME

  Enzyme nomenclature database

• • • Population genetics

  • • Software tool

  Arlequin

  An integrated software for population genetics data analysis

• • • Proteins & Proteomes

  • • Database

  UniProtKB

  Protein sequence database

• • • Systems Biology

  • • Software tool

  CLASTR

  Cellosaurus STR similarity search tool

• • • Genomics

  • • Software tool

  FastEpistasis

  Tool for quantitative trait epistasis

• • • Genomics

  • • Software tool

  TASer

  Search tool associated to TASmania

• • • Genomics
  • • Evolution biology

  • • Software tool

  CT-CBN

  Estimate conjunctive Bayesian networks

• • • Genes & Genomes
    • , Genomics
  • • Systems Biology

  • • Database
  • • Software tool

  Progenetix

  Genomic profiles of cancer samples with focus on CNV

• • • Text mining & Machine learning

  • • Software tool

  BiotXplorer

  Biotic interactions from scientific publications

• • • Genomics
  • • Evolution biology
    • , Population genetics

  • • Software tool

  fastsimcoal

  Fast sequential Markov coalescent simulation of genomic data

• • • Genomics
    • , Transcriptomics

  • • Software tool

  QuasR

  Quantification and analysis of Short Reads

• • • Proteins & Proteomes

  • • Software tool

  Myristoylator

  N-terminal myristoylation of proteins by neural networks

• • • Medicinal chemistry

  • • Software tool

  SwissSimilarity

  Ligand-based virtual screening

• • • Transcriptomics
  • • Systems Biology

  • • Software tool

  Sanity

  Single-cell RNA-Seq normalization method

• • • Genomics

  • • Database

  TASmania

  Toxin-antitoxin database

• • • Proteins & Proteomes

  • • Software tool

  Decrease redundancy

  Redundancy reduction in a set of sequences

• • • Proteins & Proteomes
  • • Systems Biology

  • • Database

  STRING SPARQL endpoint

  SPARQL access to the STRING knowledgebase

• • • Proteins & Proteomes

  • • Software tool

  FindMod

  Potential PTMs and single amino acid substitutions

• • • Evolution & Phylogeny

  • • Software tool

  raxmlGUI

  raxmlGUI 2.0 is a graphical user interface to RAxML

• • • Proteins & Proteomes

  • • Software tool

  PeptideCutter

  Potential cleavage sites in a protein

• • • Genomics

  • • Software tool

  IScan

  Insertion sequence identification in whole genomes

• • • Proteins & Proteomes

  • • Software tool

  ProtScale

  Profile produced by amino acids scales on protein sequences

• • • Genomics
    • , Transcriptomics

  • • Database

  Glittr

  Git repositories with bioinformatics training material

• • • Genes & Genomes
  • • Systems Biology

  • • Software tool

  CREMA

  Cis-Regulatory Element Motif Activities

• • • Transcriptomics

  • • Software tool

  ISA

  Finding modules in gene expression data

• • • Evolution & Phylogeny

  • • Database

  OMA SPARQL endpoint

  SPARQL access to the OMA Orthology database

• • • Proteins & Proteomes
  • • Structural Biology
    • , Structural analysis

  • • Software tool

  SWISS-MODEL Workspace

  Fully automated protein structure homology-modeling server

• • • Transcriptomics
  • • Systems Biology

  • • Software tool

  DWT-online

  Dinucleotide Weight Tensor toolbox and visualisation service

• • • Genomics

  • • Database

  EPD

  Eukaryotic Promoter Database

• • • Proteins & Proteomes

  • • Database

  UniProt SPARQL endpoint

  SPARQL access to UniProt and related data

• • • Transcriptomics
  • • Systems Biology

  • • Software tool

  Cellstates

  Infering clusters of cells in scRNA-seq data

• • • Proteins & Proteomes

  • • Software tool

  UniProt ClustalO

  Align two or more protein sequences

• • • Systems Biology

  • • Software tool

  Genome History

  Gene duplicate identification

• • • Proteins & Proteomes
  • • Systems Biology
    • , Metabolomics

  • • Database

  Rhea SPARQL endpoint

  SPARQL access to the Rhea knowledgebase

• • • Proteins & Proteomes

  • • Software tool

  ScanProsite

  Protein sequences against PROSITE

• • • Transcriptomics

  • • Database

  PolyAsite

  Database of curated RNA polyadenylation sites

• • • Genomics

  • • Database

  Pathoplexus

  Human viral pathogen genomic data sharing platform

• • • Genomics

  • • Database
  • • Software tool

  SNP2TFBS

  Regulatory SNPs affecting TF binding site affinity

• • • Proteins & Proteomes
  • • Medicinal chemistry
    • , Structural analysis

  • • Database

  SwissBioIsostere

  Database of molecular replacements for ligand design

• • • Genomics

  • • Software tool

  PACMAN

  Publication quality images of DNA locations

• • • Proteins & Proteomes
  • • Metabolomics

  • • Database
  • • Software tool

  MetaNetX

  Metabolic network repository & analysis

• • • Genomics

  • • Software tool

  ShoRAH

  Analysis of NGS data

• • • Proteins & Proteomes
  • • Medicinal chemistry
    • , Structural analysis

  • • Database

  SwissSidechain

  Database of non-natural amino acid side chains

• • • Genes & Genomes

  • • Software tool

  ESTscan

  Detect coding regions in EST sequences

• • • Evolution & Phylogeny

  • • Database

  Swiss-Trees

  A collection of gold standard gene phylogenies

• • • Genomics
  • • Proteins & Proteomes

  • • Database

  ABCD

  Database of chemically defined antibodies

• • • Proteins & Proteomes

  • • Software tool

  pROC

  Visualize, smooth and compare ROC curves

• • • Medicinal chemistry

  • • Software tool

  SwissADME

  Pharmacokinetics properties and druglikeness

• • • Text mining & Machine learning

  • • Software tool

  Variomes

  Search engine to support the curation of genomic variants

• • • Genomics

  • • Software tool

  TagScan

  Genome-wide sequence tag scanner

• • • Systems Biology

  • • Database

  Cellosaurus SPARQL endpoint

  SPARQL access to Cellosaurus

• • • 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

• • • Evolution & Phylogeny

  • • Database

  OrthoDB

  Ortholog evolutionary and functional annotations

• • • Genes & Genomes
    • , Genomics
    • , Metagenomics

  • • Software tool

  mVIRs

  Prediction tool for inducible, bacteria-infecting viruses

• • • Glycomics

  • • Software tool

  GlycoDigest

  In silico digestion of glycans by exoglycosidases

• • • Evolution & Phylogeny

  • • Database
  • • Software tool

  OMA

  Orthology inference among complete genomes

• • • Glycomics

  • • Database

  SugarBind

  Pathogen Sugar-Binding Database

• • • Proteins & Proteomes

  • • Software tool

  MALDIPepQuant

  Quantify MALDI peptides from Phenyx output

• • • Proteins & Proteomes

  • • Database
  • • Software tool

  PaxDb

  Protein abundance across several organisms

• • • Proteins & Proteomes

  • • Software tool

  Sulfinator

  Predict tyrosine sulfation sites in protein sequences

• • • Glycomics

  • • Software tool

  SugarSketcher

  Fast, intuitive, SNFG-compliant glycan structure drawing

• • • Genes & Genomes
    • , Genomics
  • • Systems Biology

  • • Database
  • • Software tool

  iPtgxDBs

  Platform for integrated proteogenomics databases

• • • Proteins & Proteomes

  • • Software tool

  pftools

  Build, calibrate, and search biological sequences

• • • Genomics
    • , Transcriptomics

  • • Software tool

  miRmap

  Prediction of microRNA target repression strength

• • • Genomics
  • • Systems Biology

  • • Database
  • • Software tool

  arrayMAP

  Curated array data repository for cancer genomics

• • • Metagenomics

  • • Software tool

  LEMMI

  Continuous benchmarking of methods for metagenomics

• • • Proteins & Proteomes

  • • Software tool

  ProtParam

  Computation of physico chemical parameters of a protein

• • • Evolution & Phylogeny

  • • Software tool

  Phylo.io

  A tool for visualising and comparing phylogenetic trees

• • • Genomics
  • • Evolution biology

  • • Software tool

  GenSpectrum

  Real-time pathogen genomic sequence analysis

• • • Genomics
    • , Transcriptomics
  • • Systems Biology

  • • Database

  SwissRegulon

  Database of genome-wide annotations of regulatory sites

• • • Proteins & Proteomes
  • • Glycomics

  • • Software tool

  GlycoMod

  Possible oligosaccharide structures on proteins from masses

• • • Glycomics

  • • Software tool

  Glynsight

  Visualise and compare glycan expression profiles

• • • Genomics
  • • Population genetics

  • • Software tool

  V-pipe SARS-CoV-2

  V-pipe pipeline for SARS-CoV-2 sequencing data

• • • Proteins & Proteomes
  • • Structural Biology

  • • Database
  • • Software tool

  CAMEO

  Weekly automated benchmarking of protein structure modelling

• • • Proteins & Proteomes
  • • Metabolomics

  • • Software tool

  rawrr

  R package for fast reading Thermo Fisher Scientific MS data

• • • Genomics

  • • Software tool

  SSA

  Analysis of nucleic acid sequence motifs

• • • 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

• • • Genomics
    • , Transcriptomics
  • • Systems Biology

  • • Software tool

  ISMARA

  Webservice for gene expression and epigenetic data analysis

• • • Glycomics

  • • Software tool

  GlycoQL

  Match a glycan substructure to a database of full structures

• • • Genomics

  • • Software tool

  MADAP

  Clustering tool of genomic sites

• • • Genomics
  • • Systems Biology

  • • Software tool

  Phylogibbs

  Regulatory sites in a collection of DNA sequences

• • • Text mining & Machine learning

  • • Software tool

  COVTriage

  Rank the COVID-19 literature according to COVoc ontology

• • • Genes & Genomes
  • • Evolution & Phylogeny

  • • Software tool

  REALPHY

  Inference of phylogenetic trees from genome data

• • • Proteins & Proteomes

  • • Database

  EnzChemRED

  Enzyme Chemistry Relation Extraction Dataset

• • • Proteins & Proteomes

  • • Software tool

  PRATT

  Conserved patterns in a set of protein sequences

• • • Glycomics

  • • Software tool

  GlyConnect Compozitor

  Contextualises glycan composition sets

• • • Genomics

  • • Software tool

  ChIP-Seq

  ChIP-Seq data analysis tools

• • • Transcriptomics

  • • Software tool

  ExpressionView

  Biclusters identified in gene expression data

• • • Genomics
  • • Evolution biology

  • • Database

  Selectome

  Database of positive selection

• • • Proteins & Proteomes
  • • Structural Biology
    • , Drug design
    • , Medicinal chemistry
    • , Structural analysis

  • • Database

  Click2Drug

  Directory of computational drug design tools

• • • Proteins & Proteomes

  • • Database

  VenomZone

  Portal to venom protein UniProtKB entries

• • • Genomics
    • , Transcriptomics

  • • Software tool

  TromER

  Prediction of transcribed regions and splice junctions

• • • Proteins & Proteomes

  • • Database
  • • Software tool

  HAMAP

  UniProtKB family classification and annotation

• • • Proteins & Proteomes

  • • Software tool

  MELANIE

  2-D PAGE analysis

• • • Proteins & Proteomes
  • • Systems Biology

  • • Database

  TCS

  Predict interaction specificity in bacterial signalling

• • • Proteins & Proteomes

  • • Software tool

  FindPept

  Unspecific protein cleavage from experimental masses

• • • Proteins & Proteomes
  • • Glycomics

  • • Database

  UniLectin

  Structural and functional classification of lectins

• • • Genes & Genomes
    • , Genomics
  • • Text mining & Machine learning

  • • Database

  cancercelllines.org

  Genomic variants in human cancer cell lines

• • • Genomics
  • • Evolution & Phylogeny

  • • Software tool

  Nextclade

  Clade assignment, mutation calling & QC for virus sequences

• • • Genomics
    • , Transcriptomics
  • • Proteins & Proteomes

  • • Software tool

  Translate

  Convert a nucleotide sequence to a protein sequence

• • • Structural analysis

  • • Software tool

  OpenStructure

  Molecular modelling and visualisation environment

• • • Genomics
    • , Transcriptomics
  • • Evolution biology

  • • Software tool

  BUSCO

  From QC to gene prediction and phylogenomics

• • • Genomics
    • , Transcriptomics

  • • Software tool

  SIBsim4

  Align expressed RNA sequences on a DNA template

• • • Evolution & Phylogeny

  • • Software tool

  OrthoLoger

  Accurate and scalable inference of groups of orthologs

• • • Proteins & Proteomes
  • • Lipidomics

  • • Database

  SwissLipids SPARQL endpoint

  SPARQL access to the SwissLipids knowledgebase

• • • Evolution & Phylogeny

  • • Database

  OrthoDB SPARQL endpoint

  SPARQL access to the OrthoDB catalog of orthologs

• • • Proteins & Proteomes
  • • Glycomics

  • • Database

  GlyConnect

  Integrated data platform to study glycosylation

• • • Systems Biology
    • , Glycomics

  • • Software tool

  HMO-Glycologue

  Simulator of Human Milk Oligosaccharide synthesis

• • • Proteins & Proteomes
  • • Structural Biology

  • • Database

  SWISS-MODEL Repository

  Protein structure homology models

• • • Proteins & Proteomes

  • • Software tool

  SIM

  Alignment of two protein sequences or within a sequence

• • • Text mining & Machine learning

  • • Database
  • • Software tool

  SIBiLS

  Personalized information retrieval from the literature

• • • Proteins & Proteomes

  • • Database

  PROSITE

  Protein family and domain database

• • • Proteins & Proteomes

  • • Software tool

  MSight

  Mass Spectrometry Imager

• • • Structural Biology

  • • Database

  ModelArchive

  Repository of predicted macromolecular structure models

• • • Transcriptomics
  • • Evolution biology

  • • Database

  Bgee SPARQL endpoint

  SPARQL access to the Bgee gene expression database

• • • Proteins & Proteomes

  • • Software tool

  RandSeq

  Random protein sequence generator

• • • Proteins & Proteomes
  • • Glycomics

  • • Software tool

  Swiss Mass Abacus

  Intuitive calculator of peptide and glycopeptide masses

• • • Proteins & Proteomes
  • • Systems Biology

  • • Database

  Protein Universe Atlas

  Interactive, annotated similarity network of all proteins

• • • Genomics
    • , Transcriptomics

  • • Software tool

  FetchGWI / tagger

  Short sequence mapping

• • • Medicinal chemistry
    • , Structural analysis

  • • Software tool

  SwissParam

  Topology and parameters for small molecules

• • • Glycomics

  • • Software tool

  Glydin'

  Network representation of known glycan determinants

• • • Proteins & Proteomes

  • • Database
  • • Software tool

  MyHits

  Relationships between protein sequences and motifs

• • • Proteins & Proteomes

  • • Software tool

  Compute pI/MW

  Isoelectric point and molecular weight from protein sequence

• • • Proteins & Proteomes

  • • Database

  neXtProt SPARQL endpoint

  SPARQL access to the neXtProt human protein knowledgebase

• • • Systems Biology

  • • Database

  SwissBioPics

  Subcellular location visualization

• • • Proteins & Proteomes

  • • Software tool

  HAMAP-Scan

  Scanning of protein sequences against HAMAP families

• • • Evolution biology

  • • Software tool

  CAPTAIN

  Decision-support tool for conservation area prioritization

• • • Proteins & Proteomes
  • • Text mining & Machine learning

  • • Database

  MHC Motif Atlas

  MHC Motif Atlas

• • • Proteins & Proteomes

  • • Software tool

  PeptideMass

  Theoretical protein cleavage by a given enzyme

• • • Systems Biology

  • • Software tool

  OMAMO

  OMAMO allows the user to find the best simple model organism

• • • Proteins & Proteomes
  • • Structural analysis

  • • Software tool

  QMEAN

  Protein model quality estimation