DC Field | Value | Language |
---|---|---|
dc.contributor.author | Lee, Kang-Hoon | ko |
dc.contributor.author | Shin, Kyung-Seop | ko |
dc.contributor.author | Lim, Debora | ko |
dc.contributor.author | Kim, Woo-Chan | ko |
dc.contributor.author | Chung, Byung Chang | ko |
dc.contributor.author | Han, GyuBum | ko |
dc.contributor.author | Roh, Jeongkyu | ko |
dc.contributor.author | Cho, Dong-Ho | ko |
dc.contributor.author | Cho, Kiho | ko |
dc.date.accessioned | 2015-07-01T02:56:17Z | - |
dc.date.available | 2015-07-01T02:56:17Z | - |
dc.date.created | 2015-06-03 | - |
dc.date.created | 2015-06-03 | - |
dc.date.created | 2015-06-03 | - |
dc.date.issued | 2015-07 | - |
dc.identifier.citation | GENOMICS, v.106, no.1, pp.30 - 42 | - |
dc.identifier.issn | 0888-7543 | - |
dc.identifier.uri | http://hdl.handle.net/10203/199617 | - |
dc.description.abstract | The genomes of living organisms are populated with pleomorphic repetitive elements (REs) of varying densities. Our hypothesis that genomic RE landscapes are species/strain/individual-specific was implemented into the Genome Signature Imaging system to visualize and compute the RE-based signatures of any genome. Following the occurrence profiling of 5-nucleotide REs/words, the information from top-50 frequency words was transformed into a genome-specific signature and visualized as Genome Signature Images (GSIs), using a CMYK scheme. An algorithm for computing distances among GSIs was formulated using the GSIs' variables (word identity, frequency, and frequency order). The utility of the GSI-distance computation system was demonstrated with control genomes. GSI-based computation of genome-relatedness among 1766 microbes (117 archaea and 1649 bacteria) identified their clustering patterns; although the majority paralleled the established classification, some did not. The Genome Signature Imaging system, with its visualization and distance computation functions, enables genome-scale evolutionary studies involving numerous genomes with varying sizes. (C) 2015 Elsevier Inc. All rights reserved. | - |
dc.language | English | - |
dc.publisher | ACADEMIC PRESS INC ELSEVIER SCIENCE | - |
dc.title | Repetitive element signature-based visualization, distance computation, and classification of 1766 microbial genomes | - |
dc.type | Article | - |
dc.identifier.wosid | 000355674900005 | - |
dc.identifier.scopusid | 2-s2.0-84930540255 | - |
dc.type.rims | ART | - |
dc.citation.volume | 106 | - |
dc.citation.issue | 1 | - |
dc.citation.beginningpage | 30 | - |
dc.citation.endingpage | 42 | - |
dc.citation.publicationname | GENOMICS | - |
dc.identifier.doi | 10.1016/j.ygeno.2015.04.004 | - |
dc.contributor.localauthor | Cho, Dong-Ho | - |
dc.contributor.nonIdAuthor | Lee, Kang-Hoon | - |
dc.contributor.nonIdAuthor | Lim, Debora | - |
dc.contributor.nonIdAuthor | Roh, Jeongkyu | - |
dc.contributor.nonIdAuthor | Cho, Kiho | - |
dc.type.journalArticle | Article | - |
dc.subject.keywordAuthor | Repetitive element | - |
dc.subject.keywordAuthor | Genome signature | - |
dc.subject.keywordAuthor | Genome visualization | - |
dc.subject.keywordAuthor | Genome distance | - |
dc.subject.keywordAuthor | Genome-scale classification | - |
dc.subject.keywordAuthor | Microbial genomes | - |
dc.subject.keywordPlus | RIBOSOMAL-RNA GENE | - |
dc.subject.keywordPlus | SQUARE HALOARCHAEON | - |
dc.subject.keywordPlus | K-MERS | - |
dc.subject.keywordPlus | SEQUENCES | - |
dc.subject.keywordPlus | ALIGNMENT | - |
dc.subject.keywordPlus | IDENTIFICATION | - |
dc.subject.keywordPlus | PHYLOGENY | - |
dc.subject.keywordPlus | EVOLUTION | - |
dc.subject.keywordPlus | BLAST | - |
dc.subject.keywordPlus | TOOL | - |
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