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dc.contributor.authorKoga, Akihikoja
dc.contributor.alternative古賀, 章彦ja
dc.date.accessioned2012-04-04T07:14:04Z-
dc.date.available2012-04-04T07:14:04Z-
dc.date.issued2012-02ja
dc.identifier.issn0831-2796ja
dc.identifier.urihttp://hdl.handle.net/2433/154764-
dc.description.abstractIt is widely accepted in a conceptual framework that repetitive sequences, especially those with high sequence homogeneity among copies, tend to be under-represented in whole-genome shotgun sequence databases, because of the difficulty of assembling sequence reads into contigs. Although this is easily inferred, there is no quantitative illustration of this phenomenon. An example using a currently used database is expected to contribute to the intuitive understanding of how serious the under-representation is. The present study provides the first quantitative example (in the case of 16 copies of virtually identical, 4.7-kb sequences in a genome of 7 × 10 (8) bp) by comparing the results of BLAST searches of a sequence database (contig N50; 9.8 kb) with those of Southern blot analysis of genomic DNA. This has revealed that the internal regions of the repetitive sequences are under-represented to a striking extent.ja
dc.format.mimetypeapplication/pdfja
dc.language.isoengja
dc.publisherCanadian Science Publishingja
dc.rights© Copyright 2012 – Canadian Science Publishing.ja
dc.rightsこの論文は著者最終稿です。内容が印刷版と異なることがありますので、引用の際には出版社版をご確認ご利用ください。This is the Accepted Author Manuscript. Please cite only the published version.ja
dc.subjectcontigja
dc.subjectdatabaseja
dc.subjectrepetitive sequencesja
dc.subjectunder-representationja
dc.subjecttransposonja
dc.titleUnder-representation of repetitive sequences in whole-genome shotgun sequence databases: an illustration using a recently acquired transposable element.ja
dc.type.niitypeJournal Articleja
dc.identifier.jtitleGenome / National Research Council Canada = Génome / Conseil national de recherches Canadaja
dc.identifier.volume55ja
dc.identifier.issue2ja
dc.identifier.spage172ja
dc.identifier.epage175ja
dc.relation.doi10.1139/g11-088ja
dc.textversionauthorja
dc.identifier.pmid22321171ja
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