MAPLE (Metabolic And Physiological potentiaL Evaluator) is an automatic system for mapping genes in an individual genome and metagenome to the functional module and for calculating the module completion ratio (MCR) in each functional module defined by Kyoto Encyclopedia of Genes and Genomes (KEGG). First, this system assigns KEGG orthology (KO) to the query genes using the KEGG automatic-annotation server (KAAS) and maps the KO-assigned genes to the KEGG functional modules automatically. After mapping of genes to modules, MAPLE automatically calculates MCR of each functional module. MAPLE can display results of comparative analyses of mapping patterns, MCR results, and abundance of completed modules not only among KEGG-annotated genomes but also between user jobs as well as between user jobs and KEGG-annotated genomes. This system has a user-friendly web interface for submission of original genomic and metagenomic data and for visual inspection of the mapping pattern and MCR results.
Metagenome or Partial Genome Sequences
KO assignment to short-read sequences (400–500 nt) produced by a high-throughput DNA sequencer is performed by KAAS using the single-directional best-hit (SBH) method. Query sequences must be translated into amino acid (aa) sequences before submission, and sequences longer than 100 aa are recommended for accurate KO assignment.
Complete or Draft Genome Sequences
KO assignment for complete gene sets that were identified in the complete genome or contigs is performed by KAAS using the bidirectional best-hit (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 results between user's jobs (metagenomic samples and individual organisms), in addition to the comparison between user’s results and KEGG-annotated genomes. The comparison results are displayed side by side.
Comparison of the KEGG‐Annotated Genomes
Comparison of KEGG-annotated genomes without user’s jobs is also possible and does not require an e-mail address.
KEGG Data used in MAPLE
MAPLE uses the following KEGG GENES and MODULE databases:
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. Encyclopedia of metagenomics, Springer-Verlag. 1-15. Doi:10.1007/978-1-s4614-6418-1_183-3, (2014) [Springer]
Last updated: Dec 24, 2014