Abstract
MetaProx is the database of metagenomic proximons: a searchable repository of proximon objects conceived with two specific goals. The first objective is to accelerate research involving metagenomic functional interactions by providing a database of metagenomic operon candidates. Proximons represent a special subset of directons (series of contiguous co-directional genes) where each member gene is in close proximity to its neighbours with respect to intergenic distance. As a result, proximons represent significant operon candidates where some subset of proximons is the set of true metagenomic operons. Proximons are well suited for the inference of metagenomic functional networks because predicted functional linkages do not rely on homology-dependent information that is frequently unavailable in metagenomic scenarios. The second objective is to explore representations for semistructured biological data that can offer an alternative to the traditional relational database approach. In particular, we use a serialized object implementation and advocate a Data as Data policy where the same serialized objects can be used at all levels (database, search tool and saved user file) without conversion or the use of human-readable markups. MetaProx currently includes 4 210 818 proximons consisting of 8 926 993 total member genes.Database URL: http://metaprox.uwaterloo.ca
Highlights
Much interest exists in the field of computational biology regarding the effective storage, dissemination and harnessing of large data sets
Metagenomic data are no exception to this trend with open-access reads in the Sequence Read Archive (SRA) [2] exceeding 100 Tb by 2011, with metagenomic sequences accounting for 11% of all bases [3]
MetaProx provides a searchable repository of proximon objects conceived with the goal of accelerating research involving metagenomic functional interactions
Summary
Much interest exists in the field of computational biology regarding the effective storage, dissemination and harnessing of large data sets. The proximon proposition constitutes an essential conceptual demarcation because the prediction of operons on the basis of gene co-direction and proximity is derived from empirical data using Escherichia coli K12 [7], and the extensibility of such a model to diverse and/or unique metagenomic taxa is currently unknown [8]. MetaProx provides a searchable repository of proximon objects (i.e. operon candidates) conceived with the goal of accelerating research involving metagenomic functional interactions (see Applications).
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