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MicroB, the largest integrated database of complete microbial genomes on the market


In MicroB, biochemical data are directly connected to genomic and proteic annotations.  This network of connections between genomes, proteomes and pathways enables you to quickly discover relationships, reconstruct metabolic systems and improve understanding of cellular processes.


MicroB’s exceptional structure & design enable you to situate your genomes in this functional context, providing you with a constantly growing and evolving network of valuable information.

 


Expand your knowledge base

 

We understand how important data compatibility, centralization, and accessibility are to research organizations. Much more than a reference database, MicroB enables you to build on and centralize your knowledge:

 

  • You can easily connect and integrate your newly analyzed genomes with the complete genomic, proteic, and biochemical data in MicroB, enriching your database with the addition of each new genome.   

 

  •  Whether you annotate your genomes using Genostar’s Metabolic Pathway Builder software or other tools, you can integrate & connect them with all the data in your MicroB database.

 

  • Your database is augmented in a traceable manner. Your data are centralized and readily available for future reference and analysis.

 

Reference data in MicroB is updated regularly to meet the needs of scientists in many areas of life sciences research, ensuring that you benefit from the most recent advances.

 

MicroB is a relational database that integrates and connects the most recent and complete genomic, proteic, biochemical and metabolic reference data available on microorganisms. It enables comparative analysis of your data in their functional context. See below for more details.

 

MicroB database content of the latest release


                 December 2013

5026 complete reference microorganisms available

 

Archaea (160)             Bacteria (2528)             Viruses (2338)

 

 

Advantages

  • Have the most complete reference data at hand to analyze your sequences and expression data in their functional context.

 

  • Explore and compare data easily with our user-friendly Metabolic Pathway Builder software. 

 

  • Add your proprietary genomes to your MicroB database in complete security and confidentiality.  

 

  • Build Blast databanks. Take advantage of a wide range of options for building Blast databanks using MicroB and our Metabolic Pathway Builder software.  Read more…

 

  • Your data is centralized and readily available for future reference or analysis whenever you or your colleagues need it.

 

  • Share your data with a click.

 

  • Benefit from regular data updates. We update and enlarge MicroB continuously to meet the needs of scientists in many areas of life sciences research. 

 

  •  Flexible installation solutions. You can install MicroB locally, or let us host it for you via a secure, Web-based connection. Read more...

 

 

Customized solutions 

We can create customized databases of up to 250 complete genomes of your choice from our MicroB database to allow you to focus on data specifically oriented to your research needs.

 

 

About the data

Annotation of publically available sequences is evolving rapidly. New genes, RNA, and other genomic features are identified on a regular basis, and main biological classifications (functional, taxonomy, & so forth) progress every month. We understand the importance of using the most accurate and up to date reference data in your research.

 

MicroB is updated continuously using trigger mechanisms for data consistency checks.  These programs verify the coherence of the data. All data and updates are then validated and tested by Genostar’s R&D team before we send them to you.

 

MicroB integrates and connects data from the following sources:

 

  • NCBI Taxonomy
  • RefSeq (NCBI)
  • UniProtKB
  • Enzyme
  • KEGG
  • Gene Ontology

 

 

 

Data types in MicroB

 

Genomic Data

Proteic Data

Metabolic Data

Complete genomes (chromosomes  &  plasmids)

Location of genomic features on both strands

  • ORFs
  • Coding sequences (CDS)
  • Pseudogenes
  • transfer RNAs
  • ribosomal RNAs
  • small RNAs:
    • transfer-messenger RNAs
    • small cytoplasmic RNAs
    • noncoding RNAs
    • miscellaneous RNAs

Translation of CDSs

Frameshifts

GC rates

Ribosome binding sites

 

Complete proteomes (non-redundant proteic sequences)

Attributions of protein origin:

  • Experimentally identified
    • Protein level
    • Transcript level
  • Inferred from homology
  • Computationally predicted

Protein functions

Localization of functional domains

  • Pfam & PROSITE identifiers

Gene Ontologies

  • Classification of protein roles in cellular context

PDB identifiers

Chemical compounds (name, structure and formula)

Biochemical reactions

  • Reactants
  • Enzymes (proteins linked to enzymatic classification)
  • Cofactors

KEGG maps

Networks of metabolic pathways connected to KEGG maps

Non-metabolic pathways

 

Classifications

Taxonomy: automatic attribution of order-genus-family-species paths by strain

Controlled vocabulary from Gene Ontology and Swiss-Prot (hierarchy of biological terms for genes, RNAs etc)

Functional classifications

Enzyme classifications

  • Assignment of catalytic domains to protein-coding genes
  • Description of catalytic activity for each enzyme-cataloged domain

Pfam & PROSITE classifications

  • Assignment of protein family domain to coding genes

 


Acknowledgements

Genostar designed MicroB in collaboration with the French National Institute for Research in Computer Science and Control (INRIA), the Swiss Institute of Bioinformatics (SIB), and the Laboratory of Alpine Ecology (LECA).

For more information about Genostar's bioinformatics services,
data and software, contact us or Email us

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