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Explore high-quality biological data resources

e.g. BLAST, UniProt, MSH6, Albumin...

## Filters

Genes & Genomes

- Genomics
- Metagenomics
- Transcriptomics

Proteins & Proteomes

Evolution & Phylogeny

- Evolution biology
- Population genetics

Structural Biology

- Drug design
- Medicinal chemistry
- Structural analysis

Systems Biology

- Glycomics
- Lipidomics
- Metabolomics

Text mining & Machine learning

## SIB Resources
Information

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.

- - - Transcriptomics
- - Evolution biology

- - Database
- - Software tool

### Bgee

Gene expression expertise
- - - Proteins & Proteomes
- - Systems Biology

- - Database
- - Software tool

### STRING

Protein-protein interaction networks and enrichment analysis
- - - Proteins & Proteomes
- - Lipidomics

- - Database

### SwissLipids

Knowledge resource for lipids
- - - Systems Biology

- - Database

### Cellosaurus

Knowledge resource on cell lines
- - - Genomics
- - Population genetics

- - Software tool

### V-pipe

Viral genomics pipeline
- - - Genomics
- - Evolution biology

- - Software tool

### Nextstrain

Impact of pathogen genome data on science and public health
- - - Metagenomics
- - Population genetics

- - Database
- - Software tool

### mOTUs

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

- - Database

### UniProtKB/Swiss-Prot

Protein knowledgebase
- - - Proteins & Proteomes
- - Metabolomics

- - Database

### Rhea

Expert-curated database of biochemical reactions
- - - Genes & Genomes
- - Evolution & Phylogeny

- - Database
- - Software tool

### SwissOrthology

One-stop shop for orthologs
- - - Medicinal chemistry

- - Database
- - Software tool

### SwissDrugDesign

Widening access to computer-aided drug design
- - - Transcriptomics
- - Evolution & Phylogeny
- - Systems Biology

- - Database
- - Software tool

### SwissRegulon Portal

Tools and data for regulatory genomics
- - - Proteins & Proteomes
- - Structural Biology

- - Database
- - Software tool

### SWISS-MODEL

Protein structure homology-modelling
- - - Transcriptomics

- - Database
- - Software tool

### ASAP

Web-based, cooperative portal for single-cell data analyses
- - - Genes & Genomes

- - Database
- - Software tool

### SPSP | Swiss Pathogen Surveillance Platform

Public Swiss pathogen NGS data
- - - Proteins & Proteomes
- - Glycomics

- - Database
- - Software tool

### Glyco@Expasy

Zooming in on web-based glycoinformatics resources
- - - Genes & Genomes
- - Evolution biology

- - Software tool

### BEAST2

Bayesian evolutionary analysis by sampling trees

## Other Resources of SIB Groups

- - - Proteins & Proteomes

- - Database

### UniProtKB

Protein sequence database
- - - Genomics
- - Evolution biology

- - Database

### Selectome

Database of positive selection
- - - Proteins & Proteomes

- - Database

### PROSITE

Protein family and domain database
- - - Proteins & Proteomes
- - Structural Biology

- - Database

### SWISS-MODEL Repository

Protein structure homology models
- - - Proteins & Proteomes
- - Medicinal chemistry

- - Software tool

### SwissDock

Docking of small ligands into protein active sites
- - - Proteins & Proteomes

- - Database

### ENZYME

Enzyme nomenclature database
- - - Proteins & Proteomes

- - Database
- - Software tool

### HAMAP

UniProtKB family classification and annotation
- - - Genes & Genomes
- - Proteins & Proteomes
- - Structural Biology

- - Database

### ViralZone

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

- - Database
- - Software tool

### neXtProt

Human protein knowledgebase
- - - Evolution & Phylogeny

- - Database

### OrthoDB

Ortholog evolutionary and functional annotations
- - - Evolution & Phylogeny

- - Database
- - Software tool

### OMA

Orthology inference among complete genomes
- - - Proteins & Proteomes
- - Metabolomics

- - Database
- - Software tool

### MetaNetX

Metabolic network repository & analysis
- - - Proteins & Proteomes

- - Database

### VenomZone

Portal to venom protein UniProtKB entries
- - - Population genetics

- - Software tool

### Arlequin

An integrated software for population genetics data analysis
- - - Proteins & Proteomes
- - Glycomics

- - Database

### UniLectin

Structural and functional classification of lectins
- - - Structural Biology
- - Glycomics

- - Database

### UniCarb-DB

Glycan structures and associated mass spectrometry data
- - - Genomics

- - Database
- - Software tool

### EPD

Eukaryotic Promoter Database
- - - Proteins & Proteomes
- - Structural analysis

- - Software tool

### SwissTargetPrediction

Target prediction for bioactive small molecules
- - - Medicinal chemistry

- - Software tool

### SwissSimilarity

Ligand-based virtual screening
- - - Proteins & Proteomes
- - Structural analysis

- - Database

### SwissSidechain

Database of non-natural amino acid side chains
- - - Transcriptomics

- - Software tool

### TagScan

Genome-wide sequence tag scanner
- - - Transcriptomics
- - Systems Biology

- - Database

### SwissRegulon

Database of genome-wide annotations of regulatory sites
- - - Structural analysis

- - Software tool

### SwissParam

Topology and parameters for small molecules
- - - Proteins & Proteomes
- - Structural analysis

- - Database

### SwissBioIsostere

Database of molecular replacements for ligand design
- - - Medicinal chemistry

- - Software tool

### SwissADME

Pharmacokinetics properties and druglikeness
- - - Glycomics

- - Software tool

### SugarSketcher

Fast, intuitive, SNFG-compliant glycan structure drawing
- - - Proteins & Proteomes
- - Glycomics

- - Database

### SugarBind

Pathogen Sugar-Binding Database
- - - Genomics

- - Software tool

### SSA

Analysis of nucleic acid sequence motifs
- - - Genomics

- - Database
- - Software tool

### SNP2TFBS

Regulatory SNPs affecting TF binding site affinity
- - - Transcriptomics

- - Software tool

### SIBsim4

Align expressed RNA sequences on a DNA template
- - - Genomics

- - Software tool

### ShoRAH

Analysis of NGS data
- - - Genes & Genomes
- - Evolution & Phylogeny

- - Software tool

### REALPHY

Inference of phylogenetic trees from genome data
- - - Transcriptomics

- - Software tool

### QuasR

Quantification and analysis of Short Reads
- - - Proteins & Proteomes
- - Structural analysis

- - Software tool

### QMEAN

Protein model quality estimation
- - - Genes & Genomes
- - Systems Biology

- - Database

### Progenetix

Genomic profiles of cancer samples with focus on CNV
- - - Proteins & Proteomes

- - Software tool

### pftools

Build, calibrate, and search biological sequences
- - - Proteins & Proteomes

- - Database
- - Software tool

### PaxDb

Protein abundance across several organisms
- - - Structural analysis

- - Software tool

### OpenStructure

Molecular modelling and visualisation environment
- - - Genomics
- - Systems Biology

- - Database

### arrayMAP

Curated array data repository for cancer genomics
- - - Proteins & Proteomes

- - Software tool

### MSight

Mass Spectrometry Imager
- - - Transcriptomics

- - Software tool

### miRmap

Prediction of microRNA target repression strength
- - - Genomics

- - Software tool

### MADAP

Clustering tool of genomic sites
- - - Genomics

- - Software tool

### IScan

Insertion sequence identification in whole genomes
- - - Genomics
- - Systems Biology

- - Database
- - Software tool

### iPtgxDBs

Platform for integrated proteogenomics databases
- - - Proteins & Proteomes

- - Software tool

### MELANIE

2-D PAGE analysis
- - - Glycomics

- - Software tool

### Glynsight

Visualise and compare glycan expression profiles
- - - Glycomics

- - Software tool

### Glydin'

Network representation of known glycan determinants
- - - Proteins & Proteomes
- - Glycomics

- - Software tool

### GlycoSiteAlign

Multiple alignment of sequences around glycosylation sites
- - - Proteins & Proteomes
- - Glycomics

- - Database

### GlyConnect

Integrated data platform to study glycosylation
- - - Genes & Genomes
- - Evolution biology

- - Software tool

### GenomeHistory

Gene duplicate identification
- - - Transcriptomics

- - Software tool

### FetchGWI / tagger

Short sequence mapping
- - - Genomics
- - Population genetics

- - Software tool

### fastsimcoal

Fast sequential Markov coalescent simulation of genomic data
- - - Genomics

- - Software tool

### FastEpistasis

Tool for quantitative trait epistasis
- - - Transcriptomics
- - Evolution biology

- - Software tool

### BUSCO

From QC to gene prediction and phylogenomics
- - - Transcriptomics
- - Proteins & Proteomes

- - Software tool

### Translate

Convert a nucleotide sequence to a protein sequence
- - - Proteins & Proteomes

- - Software tool

### Sulfinator

Predict tyrosine sulfation sites in protein sequences
- - - Proteins & Proteomes

- - Software tool

### SIM

Alignment of two protein sequences or within a sequence
- - - Proteins & Proteomes

- - Software tool

### RandSeq

Random protein sequence generator
- - - Proteins & Proteomes

- - Software tool

### ProtScale

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

- - Database

### ABCD

Database of chemically defined antibodies
- - - Proteins & Proteomes

- - Software tool

### ProtParam

Computation of physico chemical parameters of a protein
- - - Proteins & Proteomes

- - Software tool

### PRATT

Conserved patterns in a set of protein sequences
- - - Proteins & Proteomes

- - Software tool

### PeptideMass

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

- - Software tool

### PeptideCutter

Potential cleavage sites in a protein
- - - Proteins & Proteomes
- - Text mining & Machine learning

- - Software tool

### Myristoylator

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

- - Software tool

### MALDIPepQuant

Quantify MALDI peptides from Phenyx output
- - - Proteins & Proteomes

- - Software tool

### HAMAP-Scan

Scanning of protein sequences against HAMAP families
- - - Proteins & Proteomes
- - Glycomics

- - Software tool

### GlycoMod

Possible oligosaccharide structures on proteins from masses
- - - Proteins & Proteomes

- - Software tool

### FindPept

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

- - Software tool

### FindMod

Potential PTMs and single amino acid substitutions
- - - Proteins & Proteomes

- - Software tool

### Decrease redundancy

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

- - Software tool

### Compute pI/MW

Isoelectric point and molecular weight from protein sequence
- - - Proteins & Proteomes

- - Software tool

### UniProt ClustalO

Align two or more protein sequences
- - - Proteins & Proteomes

- - Software tool

### UniProt BLAST

BLAST sequence similarity search on the UniProt web site
- - - Genomics

- - Database
- - Software tool

### ChIP-Seq

ChIP-Seq data analysis tools
- - - Proteins & Proteomes
- - Structural analysis

- - Database

### Click2Drug

Directory of computational drug design tools
- - - Transcriptomics
- - Systems Biology

- - Software tool

### CRUNCH

Automated pipeline for ChIP-seq data analysis
- - - Proteins & Proteomes

- - Software tool

### Dotlet

Regions of close similarity in 2 sequences
- - - Systems Biology

- - Software tool

### CLASTR

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

- - Software tool

### SWISS-MODEL Workspace

Fully automated protein structure homology-modeling server
- - - Proteins & Proteomes
- - Systems Biology

- - Database

### TCS

Predict interaction specificity in bacterial signalling
- - - Genomics
- - Evolution biology

- - Software tool

### CT-CBN

Estimate conjunctive Bayesian networks
- - - Transcriptomics
- - Systems Biology

- - Software tool

### ISA

Finding modules in gene expression data
- - - Transcriptomics
- - Systems Biology

- - Software tool

### ExpressionView

Biclusters identified in gene expression data
- - - Transcriptomics
- - Systems Biology

- - Software tool

### ISMARA

Webservice for gene expression and epigenetic data analysis
- - - Genomics
- - Systems Biology

- - Software tool

### Phylogibbs

Regulatory sites in a collection of DNA sequences
- - - Proteins & Proteomes

- - Software tool

### ScanProsite

Protein sequences against PROSITE
- - - Genomics
- - Population genetics

- - Software tool

### V-pipe SARS-CoV-2

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

- - Database

### TASmania

Toxin-antitoxin database
- - - Genomics

- - Software tool

### TASer

Search tool associated to TASmania
- - - Evolution & Phylogeny

- - Database

### OMA SPARQL endpoint

SPARQL access to the OMA Orthology database
- - - Transcriptomics
- - Evolution biology

- - Database

### Bgee SPARQL endpoint

SPARQL access to the Bgee gene expression database
- - - Evolution & Phylogeny

- - Database

### OrthoDB SPARQL endpoint

SPARQL access to the OrthoDB catalog of orthologs
- - - Metagenomics

- - Software tool

### LEMMI

Continuous benchmarking of methods for metagenomics
- - - Proteins & Proteomes

- - Database

### HAMAP SPARQL endpoint

SPARQL access to the HAMAP annotation rules
- - - Proteins & Proteomes

- - Database

### UniProt SPARQL endpoint

SPARQL access to UniProt and related data
- - - Evolution & Phylogeny

- - Software tool

### OrthoLoger

Accurate and scalable inference of groups of orthologs
- - - Proteins & Proteomes

- - Software tool

### rawrr

R package for fast reading Thermo Fisher Scientific MS data
- - - Transcriptomics

- - Database

### PolyAsite

Database of curated RNA polyadenylation sites
- - - Proteins & Proteomes
- - Metabolomics

- - Database

### Rhea SPARQL endpoint

SPARQL access to the Rhea knowledgebase
- - - Text mining & Machine learning

- - Database
- - Software tool

### SIBiLS

Personalized information retrieval from the literature
- - - Proteins & Proteomes
- - Glycomics

- - Database

### GAG-DB

3D structures of glycosaminoglycans
- - - Evolution & Phylogeny

- - Software tool

### raxmlGUI

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

- - Software tool

### GlyConnect Compozitor

Contextualises glycan composition sets
- - - Glycomics

- - Software tool

### HMO-Glycologue

Simulator of Human Milk Oligosaccharide synthesis
- - - Text mining & Machine learning

- - Software tool

### Variomes

Search engine to support the curation of genomic variants
- - - Metagenomics

- - Software tool

### mVIRs

Prediction tool for inducible, bacteria-infecting viruses
- - - Systems Biology

- - Software tool

### OMAMO

OMAMO allows the user to find the best simple model organism
- - - Evolution & Phylogeny

- - Software tool

### Phylo.io

A tool for visualising and comparing phylogenetic trees
- - - Evolution & Phylogeny

- - Database

### SwissTree

A collection of gold standard gene phylogenies
- - - Genomics
- - Evolution & Phylogeny

- - Software tool

### Nextclade

Clade assignment, mutation calling & QC for virus sequences
- - - Proteins & Proteomes
- - Lipidomics

- - Database

### SwissLipids SPARQL endpoint

SPARQL access to the SwissLipids knowledgebase
- - - Proteins & Proteomes
- - Metabolomics

- - Database

### MetaNetX SPARQL endpoint

SPARQL access to MetaNetX
- - - Systems Biology

- - Database

### SwissBioPics

Subcellular location visualization
- - - Proteins & Proteomes
- - Text mining & Machine learning

- - Database

### MHC Motif Atlas

MHC Motif Atlas
- - - Structural Biology

- - Database

### ModelArchive

Repository of predicted macromolecular structure models
- - - Proteins & Proteomes
- - Structural Biology

- - Database
- - Software tool

### CAMEO

Weekly automated benchmarking of protein structure modelling
- - - Evolution biology
- - Systems Biology
- - Text mining & Machine learning

- - Software tool

### CAPTAIN

Decision-support tool for conservation area prioritization
- - - Transcriptomics

- - Database

### Glittr

Git repositories with bioinformatics training material
- - - Genes & Genomes
- - Systems Biology

- - Database

### cancercelllines.org

Genomic variants in human cancer cell lines
- - - Genes & Genomes
- - Systems Biology

- - Software tool

### CREMA

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

- - Software tool

### DWT-online

Dinucleotide Weight Tensor toolbox and visualisation service
- - - Systems Biology

- - Database

### Cellosaurus SPARQL endpoint

SPARQL access to Cellosaurus
- - - Genomics
- - Evolution biology

- - Software tool

### GenSpectrum

Real-time pathogen genomic sequence analysis
- - - Proteins & Proteomes
- - Systems Biology

- - Database

### Protein Universe Atlas

Interactive, annotated similarity network of all proteins
- - - Proteins & Proteomes

- - Software tool

### OMArk

OMArk determines the quality and completeness of gene sets
- - - Text mining & Machine learning

- - Database

### SIBiLS SPARQL endpoint

SPARQL access to SIBiLS, the SIB Literature Services
- - - Text mining & Machine learning

- - Software tool

### BiotXplorer

Biotic interactions from scientific publications
- - - Text mining & Machine learning

- - Software tool

### Biodiversity PMC

Search a large collection of scientific publications
- - - Proteins & Proteomes
- - Text mining & Machine learning

- - Database

### EnzChemRED

Enzyme Chemistry Relation Extraction Dataset
- - - Glycomics

- - Software tool

### GlycoQL

Match a glycan substructure to a database of full structures
- - - Genomics

- - Database

### Pathoplexus

Human viral pathogen genomic data sharing platform
- - - Transcriptomics
- - Systems Biology

- - Software tool

### Cellstates

Infering clusters of cells in scRNA-seq data
- - - Transcriptomics
- - Systems Biology

- - Software tool

### Sanity

Single-cell RNA-Seq normalization method
- - - Proteins & Proteomes
- - Glycomics

- - Database

### MatrixDB

Extracellular proteins and polysaccharides interactions
- - - Proteins & Proteomes

- - Software tool

### prolfqua

R package for protein differential expression analysis
- - - Metagenomics

- - Database
- - Software tool

### Microbe Atlas

Explore the microbiome of the world
- - - Proteins & Proteomes
- - Evolution & Phylogeny

- - Software tool

### OMAmer

Alignment-free protein subfamily assignment
- - - Transcriptomics
- - Systems Biology

- - Software tool

### Bonsai

Analysis of single cell RNA-seq data
- - - Structural Biology
- - Systems Biology

- - Software tool

### SimuCell3D

Tissue simulation in 3D
- - - Structural Biology
- - Systems Biology

- - Software tool

### PolyHoop

Cell and tissue dynamics simulation in 2D
- - - Proteins & Proteomes
- - Text mining & Machine learning

- - Database
- - Software tool

### MixTCRpred

Predictor of TCR-epitope interactions
- - - Evolution biology
- - Systems Biology

- - Database

### MoultDB

Integrative resource on moulting in arthropods
- - - Metagenomics

- - Software tool

### MAGFlow/BIgMAG

Metagenome metrics and taxonomical annotation visualization
- - - Transcriptomics

- - Database
- - Software tool

### Fly Cell Atlas

Single-cell transcriptomes of the entire adult Drosophila
- - - Transcriptomics

- - Database
- - Software tool

### Human Cell Atlas

Mapping the human body at the cellular level
- - - Proteins & Proteomes

- - Software tool

### MyDomains

Protein domains image creator
- - - Metagenomics

- - Database

### BeeBiome

Bee-associated microbes/viruses
- - - Genomics

- - Software tool

### Loculus

Powering microbial genome databases
- - - Transcriptomics
- - Proteins & Proteomes
- - Systems Biology

- - Software tool

### NOODAI

Multi-omics data analysis and integration
- - - Genes & Genomes
- - Proteins & Proteomes

- - Software tool

### MetaGraph

Petabase-scale sequence search
- - - Proteins & Proteomes
- - Evolution & Phylogeny

- - Database
- - Software tool

### Orthology Benchmarking

Quest for Orthologs benchmarking service

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