Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

Simple item page
dc.contributor.authorLiu, Bo
dc.contributor.authorGibbons, Theodore
dc.contributor.authorGhodsi, Mohammad
dc.contributor.authorTreangen, Todd
dc.contributor.authorPop, Mihai
dc.date.accessioned2021-11-02T14:06:18Z
dc.date.available2021-11-02T14:06:18Z
dc.date.issued2011-07-27
dc.description.abstractA major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences in the copy number of the gene between even closely related organisms, and due to PCR artifacts. The taxonomic composition can also be determined from metagenomic shotgun sequencing data by matching individual reads against a database of reference sequences. One major limitation of prior computational methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels. We propose that better classification results can be obtained by tuning the taxonomic classifier to each matching length, reference gene, and taxonomic level. We present a novel taxonomic classifier MetaPhyler (http://metaphyler.cbcb.umd.edu), which uses phylogenetic marker genes as a taxonomic reference. Results on simulated datasets demonstrate that MetaPhyler outperforms other tools commonly used in this context (CARMA, Megan and PhymmBL). We also present interesting results by analyzing a real metagenomic dataset. We have introduced a novel taxonomic classification method for analyzing the microbial diversity from whole-metagenome shotgun sequences. Compared with previous approaches, MetaPhyler is much more accurate in estimating the phylogenetic composition. In addition, we have shown that MetaPhyler can be used to guide the discovery of novel organisms from metagenomic samples.en_US
dc.description.urihttps://doi.org/10.1186/1471-2164-12-S2-S4
dc.identifierhttps://doi.org/10.13016/qsjg-i9of
dc.identifier.citationLiu, B., Gibbons, T., Ghodsi, M. et al. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics 12, S4 (2011).en_US
dc.identifier.urihttp://hdl.handle.net/1903/28088
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCollege of Computer, Mathematical & Natural Sciencesen_us
dc.relation.isAvailableAtComputer Scienceen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectMetagenomic Sequenceen_US
dc.subjectMetagenomic Studyen_US
dc.subjectTaxonomic Classifieren_US
dc.subjectGood Classification Resulten_US
dc.subjectTaxonomic Profileen_US
dc.titleAccurate and fast estimation of taxonomic profiles from metagenomic shotgun sequencesen_US
dc.typeArticleen_US

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
1471-2164-12-S2-S4.pdf
Size:
1.93 MB
Format:
Adobe Portable Document Format
Description:
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.57 KB
Format:
Item-specific license agreed upon to submission
Description:
Download

Collections

Computer Science Research Works
Biology Research Works