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Services


The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers (here only a few of them are listed). Please refer to the corresponding publications.

All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH.

Status: Actively maintained, Running, New (since 2014).

Resources & Tools

Abbr. Full name Functions Publications
STRING Search Tool for the Retrieval of Interacting Genes/Proteins Analysis of known and predicted protein-protein interactions in all known genomes
  • 2019: STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
  • 2017: The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
  • 2006: STRING 7--recent developments in the integration and prediction of protein interactions.
  • 2000: STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
  • SMART Simple Modular Architecture Research Tool Domain analysis
  • 2018: 20 years of the SMART protein domain annotation resource.
  • 2006: SMART 5: domains in the context of genomes and networks.
  • 1998: SMART, a simple modular architecture research tool: Identification of signaling domains
  • eggNOG evolutionary genealogy of genes: Non-supervised Orthologous Groups a database of orthologous groups of genes
  • 2019: eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
  • 2016: eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
  • 2014: eggNOG v4.0: nested orthology inference across 3686 organisms.
  • 2008: eggNOG: automated construction and annotation of orthologous groups of genes.
  • iPath Interactive Pathways Explorer interactive exploration of biochemical pathways and networks.
  • 2018: iPath3.0: interactive pathways explorer v3.
  • 2011: iPath2.0: interactive pathway explorer.
  • 2008: iPath: interactive exploration of biochemical pathways and networks.
  • iTOL interactive Tree Of Life an online tool for the display and manipulation of phylogenetic trees.
  • 2016: Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.
  • 2007: Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
  • STITCH Search Tool for Interactions of Chemicals Database of known and predicted interactions of chemicals and proteins.
  • 2016: STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
  • 2008: STITCH: interaction networks of chemicals and proteins.
  • mOTU Metagenomic species profiling Metagenomics
  • 2019: Microbial abundance, activity and population genomic profiling with mOTUs2.
  • 2013: Metagenomic species profiling using universal phylogenetic marker genes.
  • Microbiome-tools Microbiome Analysis Tools Developed at EMBL Microbiome Analysis
  • 2017
  • NGLess NGS Processing with Less Work NGS data processing
  • 2017
  • proGenomes A resource for consistent functional and taxonomic annotations of prokaryotic genomes. Genome Analsis
  • 2017: proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
  • metaSNV A tool for metagenomic strain level analysis. metagenomic strain analysis
  • 2017: metaSNV: A tool for metagenomic strain level analysis.
  • MOCAT a metagenomic assembly, annotation and profiling framework. metagenomic assembly & annotation
  • 2016: MOCAT2: a metagenomic assembly, annotation and profiling framework.
  • 2012: MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit.
  • Suppl. to variablecomplexes Supplimentary information Protein complex stoichiometry
  • 2016: Spatiotemporal variation of mammalian protein complex stoichiometries.
  • CART a chemical annotation retrieval toolkit. Chemical annotation retrieval
  • 2016: CART-a chemical annotation retrieval toolkit.
  • ETE 3 Reconstruction, Analysis, and Visualization of Phylogenomic Data. Phylogeny
  • 2016: ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.
  • PTMcode A resource for functional associations of post-translational modifications within and between proteins. PTM analysis
  • 2015: PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
  • 2013: PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins.
  • Companion website Companion website for TaraOcean's paper TaraOcean Project
  • 2015: Structure and function of the global ocean microbiome.
  • Enterotyping Enterotyping : R tutorials Metagenomics
  • 2015: Enterotypes of the human gut microbiome.
  • SIDER The SIDER database of drugs and side effects. Drug side effects
  • 2013: Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding
  • CODIM Characterization of drug-induced transcriptional modules Drug-induced transcription modules
  • 2013: Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding.
  • specI A species identification tool Prokaryotic species analysis
  • 2013: Accurate and universal delineation of prokaryotic species.
  • Chaetomium thermophilum genome resource The first complete genome of a true thermophilic eukaryote Genomics
  • 2011: Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile.
  • iMyco Interactive Mycoplasma Interactive Pathways Explorer dedicated to Mycoplasma pneumoniae
    Medusa a general graph visualization tool. Medusa will give users greater freedom in manipulating STRING data.
  • Medusa: a simple tool for interaction graph analysis.
  • AQUA AQUA: automatic quality improvment for multiple sequence alignment: Alignment tool
  • AQUA: Automated quality improvement for multiple sequence alignments.
  • PAL2NAL Sequence/Gene analysis Conversion of protein sequence alignments into the codon alignments + Ka/Ks-Calculations.
  • Robust conversion of protein sequence alignments into the corresponding codon alignments.
  • PolyPhen Polymorphism Phenotyping prediction of functional effect of human nsSNPs
  • Human non-synonymous SNPs: server and survey
  • BLAST2GENE
    Gene analysis in genomic regions
  • BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
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