An automated system for evaluation of the potential functionome: MAPLE version 2.1.0
نویسندگان
چکیده
Metabolic and physiological potential evaluator (MAPLE) is an automatic system that can perform a series of steps used in the evaluation of potential comprehensive functions (functionome) harboured in the genome and metagenome. MAPLE first assigns KEGG Orthology (KO) to the query gene, maps the KO-assigned genes to the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules, and then calculates the module completion ratio (MCR) of each functional module to characterize the potential functionome in the user's own genomic and metagenomic data. In this study, we added two more useful functions to calculate module abundance and Q-value, which indicate the functional abundance and statistical significance of the MCR results, respectively, to the new version of MAPLE for more detailed comparative genomic and metagenomic analyses. Consequently, MAPLE version 2.1.0 reported significant differences in the potential functionome, functional abundance, and diversity of contributors to each function among four metagenomic datasets generated by the global ocean sampling expedition, one of the most popular environmental samples to use with this system. MAPLE version 2.1.0 is now available through the web interface (http://www.genome.jp/tools/maple/) 17 June 2016, date last accessed.
منابع مشابه
Computer Algebra Meets Automated Theorem Proving: Integrating Maple and PVS
We describe an interface between version 6 of the Maple computer algebra system with the PVS automated theorem prover. The interface is designed to allow Maple users access to the robust and checkable proof environment of PVS. We also extend this environment by the provision of a library of proof strategies for use in real analysis. We demonstrate examples using the interface and the real analy...
متن کاملSecure Bio-Cryptographic Authentication System for Cardless Automated Teller Machines
Security is a vital issue in the usage of Automated Teller Machine (ATM) for cash, cashless and many off the counter banking transactions. Weaknesses in the use of ATM machine could not only lead to loss of customer’s data confidentiality and integrity but also breach in the verification of user’s authentication. Several challenges are associated with the use of ATM smart card such as: card clo...
متن کاملCost Function Modelling for Semi-automated SC, RTG and Automated and Semi-automated RMG Container Yard Operating Systems
This study analyses the concept of cost functions for semi-automated Straddle Carrier (SC), Rubber Tyred Gantry (RTG) and automated Rail Mounted Gantry (RMG) container yard operating cranes. It develops a generic cost based model for a pair-wise comparison, analysis and evaluation of economic efficiency and effectiveness of container yard equipment to be used for decision-making by terminal pla...
متن کاملRetrieval–travel-time model for free-fall-flow-rack automated storage and retrieval system
Automated storage and retrieval systems (AS/RSs) are material handling systems that are frequently used in manufacturing and distribution centers. The modelling of the retrieval–travel time of an AS/RS (expected product delivery time) is practically important, because it allows us to evaluate and improve the system throughput. The free-fall-flow-rack AS/RS has emerged as a new technology for dr...
متن کاملAn automatic test case generator for evaluating implementation of access control policies
One of the main requirements for providing software security is the enforcement of access control policies which aim to protect resources of the system against unauthorized accesses. Any error in the implementation of such policies may lead to undesirable outcomes. For testing the implementation of access control policies, it is preferred to use automated methods which are faster and more relia...
متن کامل