|Title:||Under-representation of repetitive sequences in whole-genome shotgun sequence databases: an illustration using a recently acquired transposable element.|
|Author's alias:||古賀, 章彦|
|Publisher:||Canadian Science Publishing|
|Journal title:||Genome / National Research Council Canada = Génome / Conseil national de recherches Canada|
|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.
|Appears in Collections:||Journal Articles|
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