Expasy, the Swiss Bioinformatics Resource Portal
Explore high-quality biological data resources
SIB Resources
Over 160 high-quality database and software tools are provided by SIB Groups to the global
life science
community. They are hosted on Expasy, SIB’s bioinformatics resource portal. Among them,
several key
resources - the SIB Resources - benefit from the Institute’s specific support. For more info
visit
https://www.sib.swiss/database-software-tools/sib-resources .
Other Resources of SIB Groups
UniProtKB
Protein sequence database
Selectome
Database of positive selection
PROSITE
Protein family and domain database
SWISS-MODEL Repository
Protein structure homology models
SwissDock
Docking of small ligands into protein active sites
ENZYME
Enzyme nomenclature database
HAMAP
UniProtKB family classification and annotation
ViralZone
Knowledgebase on virus biology and viral proteins
neXtProt
Human protein knowledgebase
OrthoDB
Ortholog evolutionary and functional annotations
OMA
Orthology inference among complete genomes
MetaNetX
Metabolic network repository & analysis
VenomZone
Portal to venom protein UniProtKB entries
Arlequin
An integrated software for population genetics data analysis
UniLectin
Structural and functional classification of lectins
UniCarb-DB
Glycan structures and associated mass spectrometry data
EPD
Eukaryotic Promoter Database
SwissTargetPrediction
Target prediction for bioactive small molecules
SwissSimilarity
Ligand-based virtual screening
SwissSidechain
Database of non-natural amino acid side chains
TagScan
Genome-wide sequence tag scanner
SwissRegulon
Database of genome-wide annotations of regulatory sites
SwissParam
Topology and parameters for small molecules
SwissBioIsostere
Database of molecular replacements for ligand design
SwissADME
Pharmacokinetics properties and druglikeness
SugarSketcher
Fast, intuitive, SNFG-compliant glycan structure drawing
SugarBind
Pathogen Sugar-Binding Database
SSA
Analysis of nucleic acid sequence motifs
SNP2TFBS
Regulatory SNPs affecting TF binding site affinity
SIBsim4
Align expressed RNA sequences on a DNA template
ShoRAH
Analysis of NGS data
REALPHY
Inference of phylogenetic trees from genome data
QuasR
Quantification and analysis of Short Reads
QMEAN
Protein model quality estimation
Progenetix
Genomic profiles of cancer samples with focus on CNV
pftools
Build, calibrate, and search biological sequences
PaxDb
Protein abundance across several organisms
OpenStructure
Molecular modelling and visualisation environment
arrayMAP
Curated array data repository for cancer genomics
MSight
Mass Spectrometry Imager
miRmap
Prediction of microRNA target repression strength
MADAP
Clustering tool of genomic sites
IScan
Insertion sequence identification in whole genomes
iPtgxDBs
Platform for integrated proteogenomics databases
MELANIE
2-D PAGE analysis
Glynsight
Visualise and compare glycan expression profiles
Glydin'
Network representation of known glycan determinants
GlycoSiteAlign
Multiple alignment of sequences around glycosylation sites
GlyConnect
Integrated data platform to study glycosylation
GenomeHistory
Gene duplicate identification
FetchGWI / tagger
Short sequence mapping
fastsimcoal
Fast sequential Markov coalescent simulation of genomic data
FastEpistasis
Tool for quantitative trait epistasis
BUSCO
From QC to gene prediction and phylogenomics
Translate
Convert a nucleotide sequence to a protein sequence
Sulfinator
Predict tyrosine sulfation sites in protein sequences
SIM
Alignment of two protein sequences or within a sequence
RandSeq
Random protein sequence generator
ProtScale
Profile produced by amino acids scales on protein sequences
ABCD
Database of chemically defined antibodies
ProtParam
Computation of physico chemical parameters of a protein
PRATT
Conserved patterns in a set of protein sequences
PeptideMass
Theoretical protein cleavage by a given enzyme
PeptideCutter
Potential cleavage sites in a protein
Myristoylator
N-terminal myristoylation of proteins by neural networks
MALDIPepQuant
Quantify MALDI peptides from Phenyx output
HAMAP-Scan
Scanning of protein sequences against HAMAP families
GlycoMod
Possible oligosaccharide structures on proteins from masses
FindPept
Unspecific protein cleavage from experimental masses
FindMod
Potential PTMs and single amino acid substitutions
Decrease redundancy
Redundancy reduction in a set of sequences
Compute pI/MW
Isoelectric point and molecular weight from protein sequence
UniProt ClustalO
Align two or more protein sequences
UniProt BLAST
BLAST sequence similarity search on the UniProt web site
ChIP-Seq
ChIP-Seq data analysis tools
Click2Drug
Directory of computational drug design tools
CRUNCH
Automated pipeline for ChIP-seq data analysis
Dotlet
Regions of close similarity in 2 sequences
CLASTR
Cellosaurus STR similarity search tool
SWISS-MODEL Workspace
Fully automated protein structure homology-modeling server
TCS
Predict interaction specificity in bacterial signalling
CT-CBN
Estimate conjunctive Bayesian networks
ISA
Finding modules in gene expression data
ExpressionView
Biclusters identified in gene expression data
ISMARA
Webservice for gene expression and epigenetic data analysis
Phylogibbs
Regulatory sites in a collection of DNA sequences
ScanProsite
Protein sequences against PROSITE
V-pipe SARS-CoV-2
V-pipe pipeline for SARS-CoV-2 sequencing data
TASmania
Toxin-antitoxin database
TASer
Search tool associated to TASmania
OMA SPARQL endpoint
SPARQL access to the OMA Orthology database
Bgee SPARQL endpoint
SPARQL access to the Bgee gene expression database
OrthoDB SPARQL endpoint
SPARQL access to the OrthoDB catalog of orthologs
LEMMI
Continuous benchmarking of methods for metagenomics
HAMAP SPARQL endpoint
SPARQL access to the HAMAP annotation rules
UniProt SPARQL endpoint
SPARQL access to UniProt and related data
OrthoLoger
Accurate and scalable inference of groups of orthologs
rawrr
R package for fast reading Thermo Fisher Scientific MS data
PolyAsite
Database of curated RNA polyadenylation sites
Rhea SPARQL endpoint
SPARQL access to the Rhea knowledgebase
SIBiLS
Personalized information retrieval from the literature
GAG-DB
3D structures of glycosaminoglycans
raxmlGUI
raxmlGUI 2.0 is a graphical user interface to RAxML
GlyConnect Compozitor
Contextualises glycan composition sets
HMO-Glycologue
Simulator of Human Milk Oligosaccharide synthesis
Variomes
Search engine to support the curation of genomic variants
mVIRs
Prediction tool for inducible, bacteria-infecting viruses
OMAMO
OMAMO allows the user to find the best simple model organism
Phylo.io
A tool for visualising and comparing phylogenetic trees
SwissTree
A collection of gold standard gene phylogenies
Nextclade
Clade assignment and quality control for viral genomes
SwissLipids SPARQL endpoint
SPARQL access to the SwissLipids knowledgebase
MetaNetX SPARQL endpoint
SPARQL access to MetaNetX
SwissBioPics
Subcellular location visualization
MHC Motif Atlas
MHC Motif Atlas
ModelArchive
Repository of predicted macromolecular structure models
CAMEO
Weekly automated benchmarking of protein structure modelling
CAPTAIN
Decision-support tool for conservation area prioritization
Glittr
Git repositories with bioinformatics training material
cancercelllines.org
Genomic variants in human cancer cell lines
CREMA
Cis-Regulatory Element Motif Activities
DWT-online
Dinucleotide Weight Tensor toolbox and visualisation service
Cellosaurus SPARQL endpoint
SPARQL access to Cellosaurus
GenSpectrum
Real-time pathogen genomic sequence analysis
Protein Universe Atlas
Interactive, annotated similarity network of all proteins
OMArk
OMArk determines the quality and completeness of gene sets
SIBiLS SPARQL endpoint
SPARQL access to SIBiLS, the SIB Literature Services
BiotXplorer
Biotic interactions from scientific publications
Biodiversity PMC
Search a large collection of scientific publications
EnzChemRED
Enzyme Chemistry Relation Extraction Dataset
GlycoQL
Match a glycan substructure to a database of full structures
Pathoplexus
Human viral pathogen genomic data sharing platform
Cellstates
Infering clusters of cells in scRNA-seq data
Sanity
Single-cell RNA-Seq normalization method
MatrixDB
Extracellular proteins and polysaccharides interactions
prolfqua
R package for protein differential expression analysis
Microbe Atlas
Explore the microbiome of the world
OMAmer
Alignment-free protein subfamily assignment
Bonsai
Analysis of single cell RNA-seq data
SimuCell3D
Tissue simulation in 3D
PolyHoop
Cell and tissue dynamics simulation in 2D
MixTCRpred
Predictor of TCR-epitope interactions
MoultDB
Integrative resource on moulting in arthropods
MAGFlow/BIgMAG
Metagenome metrics and taxonomical annotation visualization
Fly Cell Atlas
Single-cell transcriptomes of the entire adult Drosophila
Human Cell Atlas
Mapping the human body at the cellular level
MyDomains
Protein domains image creator
BeeBiome
Bee-associated microbes/viruses
Loculus
Infrastructure for managing pathogen genomic data
NOODAI
Multi-omics data analysis and integration
MetaGraph
Petabase-scale sequence search
Orthology Benchmarking
Quest for Orthologs benchmarking service
SPHN Metadata Catalog
Central access point for FAIR health datasets in Switzerland
SPHN SPARQL endpoint
SPARQL access to the SPHN data
HuMSub Catalog
Human gut microbiota subspecies catalog
Foldtree
Phylogenetic tree from predicted protein structures
FastOMA
Orthology inference at scale
BindCraft
Design of functional protein binders
RECOPHY
Recombination pattern analysis based on phylogeny
TEA
The Embedded Alphabet for proteins
STUN
Simulation on TUnable fitNess landscapes
PBI-Scope
Phages Bacteria Interaction exploration and overview
SPSP SPARQL endpoint
SPARQL access to the Swiss Pathogen Surveillance Platform