Bioremediation of pollutant compounds in soil and water by microorganisms is a very important discipline from both theoretical and practical points of view. This area requires integration of huge amounts of data coming from:

  • Chemical structure and reactivity of organic compounds.
  • Sequence, structure and function of proteins (enzymes).
  • Comparative genomics.
  • Environmental microbiology, etc.






MetaRouter is a system for maintaining the heterogeneous information related to biodegradation within a framework that allows its query, modification and mining.

It includes much information that grows by automatic retrieval from public databases or by manual interactive insertion by the user. The data is linked internally and with external databases.

Mining this data is carried out by the pathfinder subsystem, which can locate biodegradative pathways for a given compound and select, among all the possible pathways, those with given characteristics (e.g. shortest one, etc.).

These features make MetaRouter an essential system for laboratories working in Microbiology and Biodegradation. It is also ideal for use as a teaching tool in courses and seminars on Bioremediation.

The system is very easy to use and maintain through its web interface.

The system has been developed by bioinformaticians with wide experience in the field and has an open and modular architecture that can be adapted to the individual requirements of each customer.







Main technical characteristics

Initial set of data items included:

  • 740 organic compounds (2,167 synonyms)
  • 820 reactions
  • 502 enzymes
  • 253 organisms

Information included for organic compounds:

  • Name
  • Synonyms
  • SMILES code
  • Molecular weight
  • Unlimited number of user-defined properties (density, evaporation rate, melting point, boiling point and water solubility are already included)
  • Formula
  • Image of the chemical structure
  • Canonical three-dimensional structure in PDB format
  • Links to other databases

Information included for chemical reactions:

  • Substrates and products
  • Enzyme
  • Links to other databases

Information included for enzymes:

  • Name
  • EC code
  • Organisms
  • Database sequence identifiers
  • Links to other databases

Pathfinder:

  • Localization of pathways from an initial set of compounds to a final one and/or to the standard metabolism
  • Selection of the pathways by length, organisms where the enzymes are present and characteristics of the implicated chemical compounds.
  • Representation of the pathways with compound name, compound image, synonyms, formula, molecular weight, SMILES code and enzyme; hyperlinked to the corresponding information for compounds, enzymes and reactions.
  • Coloring pathways according with compound properties and/or enzymatic classes.

Interface:

  • Web interface
  • Querying and administration through web forms or directly via SQL statements

For more information please call us on +34 91 141 71 50 or send an email to .






2002 ALMA Bioinformatics, SL. All rights reserved.