ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun

Ruiqiang Li; Jia Ye; Songgang Li; Jing Wang; Yujun Han; Chen Ye; Jian Wang; Huanming Yang; Jun Yu; Gane Ka Shu Wong; Jun Wang

doi:10.1371/journal.pcbi.0010043

ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun

Ruiqiang Li
, Jia Ye
, Songgang Li
, Jing Wang
, Yujun Han
, Chen Ye
, Jian Wang
, Huanming Yang
, Jun Yu
, Gane Ka Shu Wong
, Jun Wang

Zhejiang University
Chinese Academy of Sciences
Peking University
University of Washington
Aarhus University
University of Southern Denmark

科研成果: 期刊稿件 › 文章 › 同行评审

92 引用（Scopus）

摘要

We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.

源语言	英语
页（从-至）	313-321
页数	9
期刊	PLoS Computational Biology
卷	1
期	4
DOI	https://doi.org/10.1371/journal.pcbi.0010043
出版状态	已出版 - 2005
已对外发布	是

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abstract = "We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.",

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AU - Ye, Jia

AU - Li, Songgang

AU - Wang, Jing

AU - Han, Yujun

AU - Ye, Chen

AU - Wang, Jian

AU - Yang, Huanming

AU - Yu, Jun

AU - Wong, Gane Ka Shu

AU - Wang, Jun

PY - 2005

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N2 - We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.

AB - We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.

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JO - PLoS Computational Biology

JF - PLoS Computational Biology

IS - 4

ER -

ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun

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