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MAPLE - Metabolic And Physiological potentiaL Evaluator

for gene mapping to the KEGG functional modules and calculation of module completion ratio (MCR)

About MAPLE

Metabolic and physiological potential evaluator (MAPLE) is an automatic system for mapping genes in the individual genome and metagenome to the functional modules defined by KEGG and for calculating the module completion ratio (MCR), the percentage of a module component filled with the input genes. It first assigns KEGG Orthology (KO) to the query genes using KEGG Automatic Annotation Server (KAAS), then maps the KO-assigned genes to the KEGG functional modules, and finally calculates MCR of each functional module. The MAPLE system provides a user-friendly web interface for submitting genomic and metagenomic data and viewing the mapping pattern and MCR results.

Metagenome or Partial Genome Sequences

KO assignment to short-read sequences (400-500nt) produced by a high throughput DNA sequencer is performed by KAAS by single-directional best hit (SBH) method. Query sequences must be translated into amino acid (aa) sequences before submission, and sequences longer than 100aa are recommended for accurate KO assignment.

Complete or Draft Genome Sequences

KO assignment for the complete gene sets identified in the complete genome or contigs is performed by KAAS by the bi-directional best hit (BBH) method.

  • - MAPLE job request (BBH method)
    • Comparison of User's Results

      Comparison of MCR results and mapping patterns to each KEGG module from multiple jobs is possible. A user can compare the results between user's jobs (metagenomic samples and individual organisms), in addition to the comparison between the user's results and the KEGG annotated genomes. The comparison results are displayed side by side in parallel.

      • - MAPLE job comparison (via e-mail)
        • Comparison of the KEGG Annotated Genomes

          Comparison of the KEGG annotated genomes without user's jobs is also possible, which does not require e-mail address to access.

          • - MAPLE genome comparison
            • KEGG Data used in MAPLE

              MAPLE uses the following KEGG GENES and MODULE databases.

              • - KEGG GENES downloaded on September 3, 2013
              • - KEGG MODULE downloaded on October 2, 2013

Example of Results

Mapping genes to the KEGG functional modules
example1

MCR calculation of each KEGG module
example2

Results comparison
example3

References

Takami H., Taniguchi T., Moriya Y., Kuwahara T., Kanehisa M. & Goto S. Evaluation method for the potential functionome harbored in the genome and metagenome. BMC Genomics. 13, 699 (2012) [pubmed] [BMC Genomics]

Takami H. New method for comparative functional genomics and metagenomics using KEGG MODULE. In: Encylopedia of Metagenomics (ed. Nelson K.) Springer (2014) in press

History

Jan 15, 2014 (Last update), MCR calculation is modified to correct calculation order.
Dec 1, 2013, site opened.