The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes

PLoS Computational Biology
Florent E AnglyF Rohwer

Abstract

Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta...Continue Reading

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Methods Mentioned

BETA
MDA
soil
Electrophoresis

Related Concepts

Viral Genome
Genome, Bacterial
Sequence Determinations, DNA
GenBank
Metagenomics
Environment
Genome
Computer Software
Software Tools
Virus

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