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dc.contributor.authorSaeed, I
dc.contributor.authorTang, S-L
dc.contributor.authorHalgamuge, SK
dc.date.accessioned2020-05-21T03:53:38Z
dc.date.available2020-05-21T03:53:38Z
dc.date.issued2012-03-01
dc.identifierpii: gkr1204
dc.identifier.citationSaeed, I., Tang, S. -L. & Halgamuge, S. K. (2012). Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition. NUCLEIC ACIDS RESEARCH, 40 (5), https://doi.org/10.1093/nar/gkr1204.
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/11343/239166
dc.description.abstractAn approach to infer the unknown microbial population structure within a metagenome is to cluster nucleotide sequences based on common patterns in base composition, otherwise referred to as binning. When functional roles are assigned to the identified populations, a deeper understanding of microbial communities can be attained, more so than gene-centric approaches that explore overall functionality. In this study, we propose an unsupervised, model-based binning method with two clustering tiers, which uses a novel transformation of the oligonucleotide frequency-derived error gradient and GC content to generate coarse groups at the first tier of clustering; and tetranucleotide frequency to refine these groups at the secondary clustering tier. The proposed method has a demonstrated improvement over PhyloPythia, S-GSOM, TACOA and TaxSOM on all three benchmarks that were used for evaluation in this study. The proposed method is then applied to a pyrosequenced metagenomic library of mud volcano sediment sampled in southwestern Taiwan, with the inferred population structure validated against complementary sequencing of 16S ribosomal RNA marker genes. Finally, the proposed method was further validated against four publicly available metagenomes, including a highly complex Antarctic whale-fall bone sample, which was previously assumed to be too complex for binning prior to functional analysis.
dc.languageEnglish
dc.publisherOXFORD UNIV PRESS
dc.titleUnsupervised discovery of microbial population structure within metagenomes using nucleotide base composition
dc.typeJournal Article
dc.identifier.doi10.1093/nar/gkr1204
melbourne.affiliation.departmentMechanical Engineering
melbourne.source.titleNUCLEIC ACIDS RESEARCH
melbourne.source.volume40
melbourne.source.issue5
dc.rights.licenseCC BY-NC
melbourne.elementsid344010
melbourne.openaccess.pmchttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3300000
melbourne.contributor.authorSAEED, ISAAM
melbourne.contributor.authorHalgamuge, Saman
dc.identifier.eissn1362-4962
melbourne.conference.locationEngland
melbourne.accessrightsOpen Access


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