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BMCBI
2011

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

10 years 5 months ago
RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles
Background: Computational analysis of metagenomes requires the taxonomical assignment of the genome contigs assembled from DNA reads of environmental samples. Because of the diverse nature of microbiomes, the length of the assemblies obtained can vary between a few hundred bp to a few hundred Kbp. Current taxonomic classification algorithms provide accurate classification for long contigs or for short fragments from organisms that have close relatives with annotated genomes. These are significant limitations for metagenome analysis because of the complexity of microbiomes and the paucity of existing annotated genomes. Results: We propose a robust taxonomic classification method, RAIphy, that uses a novel sequence similarity metric with iterative refinement of taxonomic models and functions effectively without these limitations. We have tested RAIphy with synthetic metagenomics data ranging between 100 bp to 50 Kbp. Within a sequence read range of 100 bp-1000 bp, the sensitivity of RAI...
Ozkan U. Nalbantoglu, Samuel F. Way, Steven H. Hin
Added 12 May 2011
Updated 12 May 2011
Type Journal
Year 2011
Where BMCBI
Authors Ozkan U. Nalbantoglu, Samuel F. Way, Steven H. Hinrichs, Khalid Sayood
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