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タイトル: | Under-representation of repetitive sequences in whole-genome shotgun sequence databases: an illustration using a recently acquired transposable element. |
著者: | Koga, Akihiko |
著者名の別形: | 古賀, 章彦 |
キーワード: | contig database repetitive sequences under-representation transposon |
発行日: | Feb-2012 |
出版者: | Canadian Science Publishing |
誌名: | Genome / National Research Council Canada |
巻: | 55 |
号: | 2 |
開始ページ: | 172 |
終了ページ: | 175 |
抄録: | 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. |
著作権等: | © 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(出版社版): | 10.1139/g11-088 |
PubMed ID: | 22321171 |
出現コレクション: | 学術雑誌掲載論文等 |
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