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dc.contributor.authorZhou, Fengfeng
dc.contributor.authorOlman, Victor
dc.contributor.authorXu, Ying
dc.date.accessioned2013-06-12T14:38:40Z
dc.date.available2013-06-12T14:38:40Z
dc.date.issued2008-12-17
dc.identifier.citationBMC Bioinformatics. 2008 Dec 17;9(1):546
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2105-9-546
dc.identifier.urihttp://hdl.handle.net/10724/19519
dc.description.abstractAbstract Background Each genome has a stable distribution of the combined frequency for each k-mer and its reverse complement measured in sequence fragments as short as 1000 bps across the whole genome, for 1<k<6. The collection of these k-mer frequency distributions is unique to each genome and termed the genome's barcode. Results We found that for each genome, the majority of its short sequence fragments have highly similar barcodes while sequence fragments with different barcodes typically correspond to genes that are horizontally transferred or highly expressed. This observation has led to new and more effective ways for addressing two challenging problems: metagenome binning problem and identification of horizontally transferred genes. Our barcode-based metagenome binning algorithm substantially improves the state of the art in terms of both binning accuracies and the scope of applicability. Other attractive properties of genomes barcodes include (a) the barcodes have different and identifiable characteristics for different classes of genomes like prokaryotes, eukaryotes, mitochondria and plastids, and (b) barcodes similarities are generally proportional to the genomes' phylogenetic closeness. Conclusion These and other properties of genomes barcodes make them a new and effective tool for studying numerous genome and metagenome analysis problems.
dc.titleBarcodes for genomes and applications
dc.typeJournal Article
dc.date.updated2013-06-07T18:36:33Z
dc.description.versionPeer Reviewed
dc.language.rfc3066en
dc.rights.holderFengfeng Zhou et al.; licensee BioMed Central Ltd.


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