Protein signature-based estimation of metagenomic abundances including all domains of life and viruses.
Bioinformatics
; 29(8): 973-80, 2013 Apr 15.
Article
em En
| MEDLINE
| ID: mdl-23418187
ABSTRACT
MOTIVATION Metagenome analysis requires tools that can estimate the taxonomic abundances in anonymous sequence data over the whole range of biological entities. Because there is usually no prior knowledge about the data composition, not only all domains of life but also viruses have to be included in taxonomic profiling. Such a full-range approach, however, is difficult to realize owing to the limited coverage of available reference data. In particular, archaea and viruses are generally not well represented by current genome databases. RESULTS:
We introduce a novel approach to taxonomic profiling of metagenomes that is based on mixture model analysis of protein signatures. Our results on simulated and real data reveal the difficulties of the existing methods when measuring achaeal or viral abundances and show the overall good profiling performance of the protein-based mixture model. As an application example, we provide a large-scale analysis of data from the Human Microbiome Project. This demonstrates the utility of our method as a first instance profiling tool for a fast estimate of the community structure.AVAILABILITY:
http//gobics.de/TaxyPro. SUPPLEMENTARY INFORMATION Supplementary Material is available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Estrutura Terciária de Proteína
/
Metagenômica
Limite:
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2013
Tipo de documento:
Article
País de afiliação:
Alemanha