SIB Swiss Institute of Bioinformatics (original) (raw)

Text mining & Machine learning

SIB Resources

• • • Genes & Genomes
  • • Evolution & Phylogeny
  • • Database
  • • Software tool
      SwissOrthology
      One-stop shop for orthologs
• • • Transcriptomics
  • • Evolution biology
  • • Database
  • • Software tool
      Bgee
      Gene expression expertise
• • • Proteins & Proteomes
  • • Lipidomics
  • • Database
      SwissLipids
      Knowledge resource for lipids
• • • Genes & Genomes
      • , Genomics
      • , Transcriptomics
  • • Evolution & Phylogeny
  • • Systems Biology
  • • Database
  • • Software tool
      SwissRegulon Portal
      Tools and data for regulatory genomics
• • • 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
• • • 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
• • • Systems Biology
  • • Database
      Cellosaurus
      Knowledge resource on cell lines
• • • Drug design
      • , Medicinal chemistry
  • • Database
  • • Software tool
      SwissDrugDesign
      Widening access to computer-aided drug design
• • • Transcriptomics
  • • Software tool
      ASAP
      Web-based, cooperative portal for single-cell data analyses
• • • Proteins & Proteomes
  • • Structural Biology
  • • Database
  • • Software tool
      SWISS-MODEL
      Protein structure homology-modelling
• • • Proteins & Proteomes
  • • Database
      UniProtKB/Swiss-Prot
      Protein knowledgebase
• • • Proteins & Proteomes
  • • Glycomics
  • • Database
      Glyco@Expasy
      Zooming in on web-based glycoinformatics resources

Other Resources of SIB Groups

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