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SIB Resources
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- Proteins & Proteomes
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- Structural Biology
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- Database
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- Software tool
SWISS-MODEL
Protein structure homology-modelling-
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- Genomics
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- Population genetics
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- Software tool
V-pipe
Viral genomics pipeline-
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- Genes & Genomes
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- Evolution & Phylogeny
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- Database
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- Software tool
SwissOrthology
One-stop shop for orthologs-
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- Proteins & Proteomes
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- Glycomics
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- Database
Glyco@Expasy
Zooming in on web-based glycoinformatics resources-
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- Proteins & Proteomes
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- Systems Biology
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- Database
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- Software tool
STRING
Protein-protein interaction networks and enrichment analysis-
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- Transcriptomics
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- Evolution biology
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- Database
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- Software tool
Bgee
Gene expression expertise-
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- Systems Biology
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- Database
Cellosaurus
Knowledge resource on cell lines-
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- Genes & Genomes
- , Genomics
- , Transcriptomics
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- Evolution & Phylogeny
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- Systems Biology
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- Database
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- Software tool
SwissRegulon Portal
Tools and data for regulatory genomics-
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- Proteins & Proteomes
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- Systems Biology
- , Metabolomics
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- Database
Rhea
Expert-curated database of biochemical reactions-
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- Genomics
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- Evolution biology
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- Software tool
Nextstrain
Impact of pathogen genome data on science and public health-
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- Proteins & Proteomes
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- Lipidomics
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- Database
SwissLipids
Knowledge resource for lipids-
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- Transcriptomics
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- Software tool
ASAP
Web-based, cooperative portal for single-cell data analyses-
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- Proteins & Proteomes
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- Database
UniProtKB/Swiss-Prot
Protein knowledgebase-
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- Drug design
- , Medicinal chemistry
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- Database
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- Software tool
SwissDrugDesign
Widening access to computer-aided drug design-
Other Resources of SIB Groups
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- Proteins & Proteomes
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- Software tool
UniProt ClustalO
Align two or more protein sequences-
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- Proteins & Proteomes
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- Software tool
HAMAP-Scan
Scanning of protein sequences against HAMAP families-
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- Structural analysis
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- Software tool
OpenStructure
Molecular modelling and visualisation environment-
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- Glycomics
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- Software tool
GlyConnect Compozitor
Contextualises glycan composition sets-
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- Genomics
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- Database
TASmania
Toxin-antitoxin database-
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- Text mining & Machine learning
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- Database
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- Software tool
SIBiLS
Personalized Information Retrieval in biomedical literature-
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- Genomics
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- Software tool
FastEpistasis
Tool for quantitative trait epistasis-
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- Proteins & Proteomes
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- Software tool
FindPept
Unspecific protein cleavage from experimental masses-
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- Proteins & Proteomes
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- Software tool
FindMod
Potential PTMs and single amino acid substitutions-
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- Genomics
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- Software tool
ChIP-Seq
ChIP-Seq data analysis tools-
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- Genes & Genomes
- , Genomics
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- Systems Biology
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- Database
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- Software tool
iPtgxDBs
Platform for integrated proteogenomics databases-
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- Proteins & Proteomes
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- Software tool
pROC
Visualize, smooth and compare ROC curves-
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- Medicinal chemistry
- , Structural analysis
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- Software tool
SwissParam
Topology and parameters for small molecules-
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- Metagenomics
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- Software tool
LEMMI
Continuous benchmarking of methods for metagenomics-
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- Glycomics
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- Database
SugarBind
Pathogen Sugar-Binding Database-
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- Population genetics
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- Software tool
Arlequin
An integrated software for population genetics data analysis-
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- Genes & Genomes
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- Evolution & Phylogeny
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- Software tool
BEAST2 - COVID-19 Monitoring
Epidemiological dynamics in real-time-
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- Medicinal chemistry
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- Software tool
SwissADME
Pharmacokinetics properties and druglikeness-
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- Proteins & Proteomes
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- Software tool
pftools
Build, calibrate, and search biological sequences-
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- Genomics
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- Software tool
SSA
Analysis of nucleic acid sequence motifs-
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- Genes & Genomes
- , Genomics
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- Text mining & Machine learning
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- Database
cancercelllines.org
Genomic variants in human cancer cell lines-
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- Proteins & Proteomes
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- Glycomics
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- Software tool
Swiss Mass Abacus
Intuitive calculator of peptide and glycopeptide masses-
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- Systems Biology
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- Software tool
OMAMO
OMAMO allows the user to find the best simple model organism-
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- Proteins & Proteomes
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- Systems Biology
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- Database
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- Software tool
MetaNetX
Metabolic network repository & analysis-
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- Genomics
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- Systems Biology
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- Database
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- Software tool
arrayMAP
Curated array data repository for cancer genomics-
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- Proteins & Proteomes
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- Database
neXtProt
Human protein knowledgebase-
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- Genes & Genomes
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- Evolution biology
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- Software tool
BEAST2
Bayesian evolutionary analysis by sampling trees-
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- Systems Biology
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- Database
SwissBioPics
Subcellular location visualization-
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- Systems Biology
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- Database
Cellosaurus SPARQL endpoint
SPARQL access to Cellosaurus via Wikidata-
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- Proteins & Proteomes
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- Software tool
Myristoylator
N-terminal myristoylation of proteins by neural networks-
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- Proteins & Proteomes
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- Database
neXtProt SPARQL endpoint
SPARQL access to the neXtProt human protein knowledgebase-
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- Proteins & Proteomes
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- Database
ENZYME
Enzyme nomenclature database-
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- Genomics
- , Transcriptomics
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- Systems Biology
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- Software tool
CRUNCH
Automated pipeline for ChIP-seq data analysis-
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- Genomics
- , Transcriptomics
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- Systems Biology
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- Software tool
ISMARA
Webservice for gene expression and epigenetic data analysis-
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- Genomics
- , Transcriptomics
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- Database
Glittr
Git repositories with bioinformatics training material-
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- Genomics
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- Evolution & Phylogeny
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- Software tool
Nextclade
Clade assignment, mutation calling & QC for virus sequences-
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- Proteins & Proteomes
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- Medicinal chemistry
- , Structural analysis
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- Database
SwissBioIsostere
Database of molecular replacements for ligand design-
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- Genomics
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- Software tool
ShoRAH
Analysis of NGS data-
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- Genes & Genomes
- , Genomics
- , Metagenomics
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- Software tool
mVIRs
Prediction tool for inducible, bacteria-infecting viruses-
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- Genomics
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- Software tool
TagScan
Genome-wide sequence tag scanner-
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- Proteins & Proteomes
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- Systems Biology
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- Database
TCS
Predict interaction specificity in bacterial signalling-
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- Genomics
- , Transcriptomics
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- Software tool
SIBsim4
Align expressed RNA sequences on a DNA template-
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- Glycomics
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- Software tool
GlyS3
Match a glycan substructure to a database of full structures-
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- Proteins & Proteomes
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- Systems Biology
- , Metabolomics
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- Database
Rhea SPARQL endpoint
SPARQL access to the Rhea knowledgebase-
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- Text mining & Machine learning
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- Software tool
Variomes
Search engine to support the curation of genomic variants-
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- Proteins & Proteomes
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- Software tool
ScanProsite
Protein sequences against PROSITE-
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- Genomics
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- Database
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- Software tool
SNP2TFBS
Regulatory SNPs affecting TF binding site affinity-
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- Glycomics
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- Software tool
GlycoDigest
In silico digestion of glycans by exoglycosidases-
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- Genes & Genomes
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- Proteins & Proteomes
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- Structural Biology
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- Database
ViralZone
Fact sheets about viruses linked to sequence databases-
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- Proteins & Proteomes
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- Software tool
RandSeq
Random protein sequence generator-
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- Glycomics
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- Database
GAG-DB
3D structures of glycosaminoglycans-
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- Proteins & Proteomes
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- Metabolomics
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- Software tool
rawrr
R package for fast reading Thermo Fisher Scientific MS data-
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- Proteins & Proteomes
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- Software tool
Compute pI/MW
Isoelectric point and molecular weight from protein sequence-
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- Glycomics
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- Software tool
EpitopeXtractor
Compare glycan structures to Glydin' network's collection-
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- Genomics
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- Software tool
PACMAN
Publication quality images of DNA locations-
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- Proteins & Proteomes
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- Systems Biology
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- Database
STRING SPARQL endpoint
SPARQL access to the STRING knowledgebase-
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- Proteins & Proteomes
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- Database
UniProtKB
Protein sequence database-
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- Structural Biology
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- Database
ModelArchive
Repository of predicted macromolecular structure models-
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- Proteins & Proteomes
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- Software tool
UniProt BLAST
BLAST sequence similarity search on the UniProt web site-
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- Proteins & Proteomes
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- Software tool
Dotlet
Regions of close similarity in 2 sequences-
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- Genomics
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- Evolution biology
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- Database
Selectome
Database of positive selection-
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- Proteins & Proteomes
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- Lipidomics
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- Database
SwissLipids SPARQL endpoint
SPARQL access to the SwissLipids knowledgebase-
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- Proteins & Proteomes
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- Glycomics
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- Software tool
MzJava
Open source Java class library to process MS fragmentation-
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- Proteins & Proteomes
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- Medicinal chemistry
- , Structural analysis
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- Software tool
SwissTargetPrediction
Target prediction for bioactive small molecules-
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- Genomics
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- Software tool
IScan
Insertion sequence identification in whole genomes-
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- Genes & Genomes
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- Software tool
ESTscan
Detect coding regions in EST sequences-
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- Transcriptomics
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- Systems Biology
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- Software tool
DWT-online
Dinucleotide Weight Tensor toolbox and visualisation service-
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- Proteins & Proteomes
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- Software tool
PeptideMass
Theoretical protein cleavage by a given enzyme-
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- Systems Biology
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- Software tool
CLASTR
Cellosaurus STR similarity search tool-
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- Genomics
- , Transcriptomics
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- Evolution biology
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- Software tool
BUSCO
From QC to gene prediction and phylogenomics-
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- Proteins & Proteomes
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- Software tool
PRATT
Conserved patterns in a set of protein sequences-
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- Proteins & Proteomes
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- Structural Biology
- , Medicinal chemistry
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- Software tool
SwissDock
Docking of small ligands into protein active sites-
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- Transcriptomics
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- Software tool
ExpressionView
Biclusters identified in gene expression data-
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- Proteins & Proteomes
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- Structural Biology
- , Structural analysis
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- Software tool
SWISS-MODEL Workspace
Fully automated protein structure homology-modeling server-
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- Genomics
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- Software tool
TASer
Search tool associated to TASmania-
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- Transcriptomics
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- Evolution biology
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- Database
Bgee SPARQL endpoint
SPARQL access to the Bgee gene expression database-
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- Genomics
- , Transcriptomics
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- Software tool
FetchGWI / tagger
Short sequence mapping-
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- Glycomics
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- Software tool
Glydin'
Network representation of known glycan determinants-
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- Proteins & Proteomes
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- Software tool
OMArk
OMArk determines the quality and completeness of gene sets-
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- Evolution & Phylogeny
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- Software tool
Phylo.io
A tool for visualising and comparing phylogenetic trees-
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- Genomics
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- Systems Biology
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- Software tool
Phylogibbs
Regulatory sites in a collection of DNA sequences-
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- Proteins & Proteomes
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- Structural Biology
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- Database
SWISS-MODEL Repository
Protein structure homology models-
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- Proteins & Proteomes
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- Glycomics
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- Software tool
GlycoSiteAlign
Multiple alignment of sequences around glycosylation sites-
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- Genomics
- , Transcriptomics
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- Systems Biology
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- Database
SwissRegulon
Database of genome-wide annotations of regulatory sites-
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- Proteins & Proteomes
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- Systems Biology
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- Database
MetaNetX SPARQL endpoint
SPARQL access to MetaNetX-
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- Evolution & Phylogeny
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- Database
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- Software tool
OMA
Orthology inference among complete genomes-
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- Proteins & Proteomes
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- Structural Biology
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- Database
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- Software tool
CAMEO
Weekly automated benchmarking of protein structure modelling-
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- Evolution & Phylogeny
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- Software tool
raxmlGUI
raxmlGUI 2.0 is a graphical user interface to RAxML-
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- Genomics
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- Evolution biology
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- Software tool
CT-CBN
Estimate conjunctive Bayesian networks-
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- Proteins & Proteomes
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- Software tool
Decrease redundancy
Redundancy reduction in a set of sequences-
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- Proteins & Proteomes
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- Glycomics
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- Database
UniLectin
Structural and functional classification of lectins-
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- Proteins & Proteomes
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- Software tool
ProtParam
Computation of physico chemical parameters of a protein-
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- Proteins & Proteomes
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- Database
-
- Software tool
PaxDb
Protein abundance across several organisms-
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- Genomics
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- Population genetics
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- Software tool
V-pipe SARS-CoV-2
V-pipe pipeline for SARS-CoV-2 sequencing data-
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- Genes & Genomes
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- Database
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- Software tool
SPSP | Swiss Pathogen Surveillance Platform
A secure NGS One-health online platform-
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- Glycomics
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- Database
UniCarb-DB
Glycan structures and associated mass spectrometry data-
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- Genomics
- , Transcriptomics
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- Software tool
QuasR
Quantification and analysis of Short Reads-
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- Proteins & Proteomes
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- Software tool
MALDIPepQuant
Quantify MALDI peptides from Phenyx output-
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- Glycomics
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- Software tool
Glynsight
Visualise and compare glycan expression profiles-
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- Evolution & Phylogeny
-
- Database
Swiss-Trees
A collection of gold standard gene phylogenies-
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- Genes & Genomes
- , Genomics
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- Systems Biology
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- Database
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- Software tool
Progenetix
Genomic profiles of cancer samples with focus on CNV-
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- Genomics
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- Evolution biology
- , Population genetics
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- Software tool
fastsimcoal
Fast sequential Markov coalescent simulation of genomic data-
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- Proteins & Proteomes
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- Database
VenomZone
Portal to venom protein UniProtKB entries-
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- Proteins & Proteomes
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- Software tool
MELANIE
2-D PAGE analysis-
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- Proteins & Proteomes
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- Text mining & Machine learning
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- Database
MHC Motif Atlas
MHC Motif Atlas-
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- Proteins & Proteomes
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- Glycomics
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- Database
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- Software tool
GlyConnect
Integrated data platform to study glycosylation-
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- Evolution & Phylogeny
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- Database
OrthoDB
Ortholog evolutionary and functional annotations-
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- Transcriptomics
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- Software tool
ISA
Finding modules in gene expression data-
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- Glycomics
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- Software tool
SugarSketcher
Fast, intuitive, SNFG-compliant glycan structure drawing-
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- Medicinal chemistry
-
- Software tool
SwissSimilarity
Ligand-based virtual screening-
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- Systems Biology
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- Software tool
Genome History
Gene duplicate identification-
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- Text mining & Machine learning
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- Software tool
Computational Linguistics for COVID-19
Central hub in computational linguistics for COVID-19-
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- Transcriptomics
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- Database
PolyAsite
Database of curated RNA polyadenylation sites-
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- Proteins & Proteomes
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- Glycomics
-
- Database
GlyConnect SPARQL endpoint
SPARQL access to GlyConnect-
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- Text mining & Machine learning
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- Database
SIBiLS SPARQL endpoint
SPARQL access to SIBiLS, the SIB Literature Services-
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- Genomics
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- Software tool
MADAP
Clustering tool of genomic sites-
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- Metabolomics
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- Software tool
MSight
Mass Spectrometry Imager-
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- Systems Biology
- , Glycomics
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- Software tool
HMO-Glycologue
Simulator of Human Milk Oligosaccharide synthesis-
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- Genomics
- , Transcriptomics
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- Software tool
TromER
Prediction of transcribed regions and splice junctions-
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- Evolution & Phylogeny
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- Database
OMA SPARQL endpoint
SPARQL access to the OMA Orthology database-
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- Proteins & Proteomes
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- Structural analysis
-
- Software tool
QMEAN
Protein model quality estimation-
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- Proteins & Proteomes
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- Software tool
PeptideCutter
Potential cleavage sites in a protein-
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- Genes & Genomes
- , Genomics
-
- Database
-
- Software tool
SVIP
Clinical interpretation of variants in cancer-
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- Proteins & Proteomes
-
- Database
-
- Software tool
MyHits
Relationships between protein sequences and motifs-
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- Genomics
- , Transcriptomics
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- Proteins & Proteomes
-
- Software tool
Translate
Nucleotide sequence to a protein sequence-
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- Evolution biology
-
- Software tool
CAPTAIN
Decision-support tool for conservation area prioritization-
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- Proteins & Proteomes
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- Software tool
SIM
Alignment of two protein sequences or within a sequence-
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- Text mining & Machine learning
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- Software tool
COVTriage
Rank the COVID-19 literature according to COVoc ontology-
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- Genes & Genomes
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- Evolution biology
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- Software tool
GenSpectrum
Real-time pathogen genomic sequence analysis-
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- Evolution & Phylogeny
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- Software tool
OrthoLoger
Accurate and scalable inference of groups of orthologs-
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- Proteins & Proteomes
-
- Database
HAMAP SPARQL endpoint
SPARQL access to the HAMAP annotation rules-
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- Proteins & Proteomes
-
- Database
PROSITE
Protein family and domain database-
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- Proteins & Proteomes
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- Database
UniProt SPARQL endpoint
SPARQL access to UniProt and related data-
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- Proteins & Proteomes
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- Database
-
- Software tool
HAMAP
UniProtKB family classification and annotation-
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- Proteins & Proteomes
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- Glycomics
-
- Software tool
GlycoMod
Possible oligosaccharide structures on proteins from masses-
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- Proteins & Proteomes
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- Structural Biology
- , Drug design
- , Medicinal chemistry
- , Structural analysis
-
- Database
Click2Drug
Directory of computational drug design tools-
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- Metagenomics
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- Population genetics
-
- Software tool
mOTUs
Microbial taxonomic and population genomic profiler-
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- Genomics
- , Transcriptomics
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- Software tool
miRmap
Prediction of microRNA target repression strength-
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- Genes & Genomes
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- Evolution & Phylogeny
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- Software tool
REALPHY
Inference of phylogenetic trees from genome data-
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- Proteins & Proteomes
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- Systems Biology
-
- Database
Protein Universe Atlas
Interactive, annotated similarity network of all proteins-
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- Proteins & Proteomes
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- Software tool
Sulfinator
Predict tyrosine sulfation sites in protein sequences-
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- Evolution & Phylogeny
-
- Database
OrthoDB SPARQL endpoint
SPARQL access to the OrthoDB catalog of orthologs-
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- Genomics
-
- Database
EPD
Eukaryotic Promoter Database-
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- Proteins & Proteomes
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- Medicinal chemistry
- , Structural analysis
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- Database
SwissSidechain
Database of non-natural amino acid side chains-
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- Genes & Genomes
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- Systems Biology
-
- Software tool
CREMA
Cis-Regulatory Element Motif Activities-
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- Proteins & Proteomes
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- Software tool
ProtScale
Profile produced by amino acids scales on protein sequences-
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- Genomics
-
- Proteins & Proteomes
-
- Database
ABCD
Database of chemically defined antibodies-