Comparison of soil bacterial community structure in rice paddy fields under different management practices using terminal restriction fragment length polymorphism (T-RFLP) = 논 토양의 세균군집구조 비교

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dc.contributor.authorDo Young Kim-
dc.contributor.authorChang-Gi Kim-
dc.contributor.authorS B Sohn-
dc.contributor.authorS Park-
dc.date.accessioned2017-04-19T09:12:51Z-
dc.date.available2017-04-19T09:12:51Z-
dc.date.issued2008-
dc.identifier.issn1225-0317-
dc.identifier.uri10.5141/JEFB.2008.31.4.309ko
dc.identifier.urihttps://oak.kribb.re.kr/handle/201005/8781-
dc.description.abstractBackground: In the study of adaptive evolution, it is important to detect the protein coding sites where natural selection is acting. In general, the ratio of the rate of non-synonymous substitutions (Ka) to the rate of synonymous substitutions (Ks) is used to estimate either negative or positive selection for an entire gene region of interest. However, since each amino acid in a region has a different function and structure, the type and strength of natural selection may be different for each amino acid. Specifically, domain sites on the protein are indicative of structurally and functionally important sites. Therefore, Window-sliding tools can be used to detect evolutionary forces acting on mutation sites. Results: This paper reports the development of a web-based tool, WSPMaker (Window-sliding Selection pressure Plot Maker), for calculating selection pressures (estimated by Ka/Ks) in the sub-regions of two protein-coding DNA sequences (CDSs). The program uses a sliding window on DNA with a user-defined window length. This enables the investigation of adaptive protein evolution and shows selective constraints of the overall/specific region(s) of two orthologous gene-coding DNA sequences. The method accommodates various evolutionary models and options such as the sliding window size. WSPmaker uses domain information from Pfam HMM models to detect highly conserved residues within orthologous proteins. Conclusion: WSPMaker is a web tool for scanning and calculating selection pressures (estimated by Ka/Ks) in sub-regions of two protein-coding DNA sequences (CDSs).-
dc.publisherKorea Soc-Assoc-Inst-
dc.titleComparison of soil bacterial community structure in rice paddy fields under different management practices using terminal restriction fragment length polymorphism (T-RFLP) = 논 토양의 세균군집구조 비교-
dc.title.alternativeComparison of soil bacterial community structure in rice paddy fields under different management practices using terminal restriction fragment length polymorphism (T-RFLP)-
dc.typeArticle-
dc.citation.titleJournal of Ecology & Field Biology-
dc.citation.number4-
dc.citation.endPage316-
dc.citation.startPage309-
dc.citation.volume31-
dc.contributor.affiliatedAuthorDo Young Kim-
dc.contributor.affiliatedAuthorChang-Gi Kim-
dc.contributor.alternativeName김도영-
dc.contributor.alternativeName김창기-
dc.contributor.alternativeName손상목-
dc.contributor.alternativeName박상규-
dc.identifier.bibliographicCitationJournal of Ecology & Field Biology, vol. 31, no. 4, pp. 309-316-
dc.identifier.doi10.5141/JEFB.2008.31.4.309-
dc.subject.keyworddiversity indices-
dc.subject.keywordorganic farming practice-
dc.subject.keywordrice paddy fields-
dc.subject.keywordsoil bacterial community-
dc.subject.keywordterminal restriction fragment length polymorphism (T-RFLP)-
dc.subject.localdiversity indices-
dc.subject.localorganic farming practice-
dc.subject.localrice paddy fields-
dc.subject.localsoil bacterial community-
dc.subject.localTerminal restriction fragment length polymorphism (T-RFLP)-
dc.subject.localterminal restriction fragment length polymorphism (T-RFLP)-
dc.description.journalClassN-
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Division of Bio Technology Innovation > Bio-Evaluation Center > 1. Journal Articles
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