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Title: Under-representation of repetitive sequences in whole-genome shotgun sequence databases: an illustration using a recently acquired transposable element.
Authors: Koga, Akihiko  kyouindb  KAKEN_id
Author's alias: 古賀, 章彦
Keywords: contig
database
repetitive sequences
under-representation
transposon
Issue Date: Feb-2012
Publisher: Canadian Science Publishing
Journal title: Genome / National Research Council Canada = Génome / Conseil national de recherches Canada
Volume: 55
Issue: 2
Start page: 172
End page: 175
Abstract: It 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.
Rights: © Copyright 2012 – Canadian Science Publishing.
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.
URI: http://hdl.handle.net/2433/154764
DOI(Published Version): 10.1139/g11-088
PubMed ID: 22321171
Appears in Collections:Journal Articles

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