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Unsupervised Two-Way Clustering of Metagenomic Sequences
Joint Authors
Acharya, Raj
Prabhakara, Shruthi
Source
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-04-05
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Abstract EN
A major challenge facing metagenomics is the development of tools for the characterization of functional and taxonomic content of vast amounts of short metagenome reads.
The efficacy of clustering methods depends on the number of reads in the dataset, the read length and relative abundances of source genomes in the microbial community.
In this paper, we formulate an unsupervised naive Bayes multispecies, multidimensional mixture model for reads from a metagenome.
We use the proposed model to cluster metagenomic reads by their species of origin and to characterize the abundance of each species.
We model the distribution of word counts along a genome as a Gaussian for shorter, frequent words and as a Poisson for longer words that are rare.
We employ either a mixture of Gaussians or mixture of Poissons to model reads within each bin.
Further, we handle the high-dimensionality and sparsity associated with the data, by grouping the set of words comprising the reads, resulting in a two-way mixture model.
Finally, we demonstrate the accuracy and applicability of this method on simulated and real metagenomes.
Our method can accurately cluster reads as short as 100 bps and is robust to varying abundances, divergences and read lengths.
American Psychological Association (APA)
Prabhakara, Shruthi& Acharya, Raj. 2012. Unsupervised Two-Way Clustering of Metagenomic Sequences. BioMed Research International،Vol. 2012, no. 2012, pp.1-11.
https://search.emarefa.net/detail/BIM-991469
Modern Language Association (MLA)
Prabhakara, Shruthi& Acharya, Raj. Unsupervised Two-Way Clustering of Metagenomic Sequences. BioMed Research International No. 2012 (2012), pp.1-11.
https://search.emarefa.net/detail/BIM-991469
American Medical Association (AMA)
Prabhakara, Shruthi& Acharya, Raj. Unsupervised Two-Way Clustering of Metagenomic Sequences. BioMed Research International. 2012. Vol. 2012, no. 2012, pp.1-11.
https://search.emarefa.net/detail/BIM-991469
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-991469