ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun.
ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun.
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DOI：
10.1371/journal.pcbi.0010043
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发表时间：
2005-09
影响因子：
4.3
通讯作者：
Wang J
中科院分区：
文献类型：
--
作者：
Li R;Ye J;Li S;Wang J;Han Y;Ye C;Wang J;Yang H;Yu J;Wong GK;Wang J
我们描述了一种算法，ReAS，用于从全基因组鸟枪法的未组装读段中恢复转座元件（TEs）的祖先序列。主要假设是这些转座元件在基因组中必须以高拷贝数存在，并且不能太古老，以至于与它们的祖先序列相比不再可识别。在粳稻基因组上进行测试时，ReAS能够重建已知转座元件的Repbase库中的所有高拷贝序列，并提高了RepeatMasker从基因组序列中识别转座元件的效率。
转座元件是多细胞生物基因组的一个主要组成部分。它们是入侵基因组、插入自身多个拷贝然后死亡的寄生生物。我们现在看到的都是它们祖先序列的退化残余。这些祖先序列的重建可以使死亡的转座元件复活。检测转座元件的算法将现今的序列与祖先序列库进行比较。很多人不知道的是，全基因组鸟枪法在大规模测序中的广泛使用使得转座元件的重建变得越来越成问题。为了将组装错误降至最低，全基因组鸟枪法必须排除大多数转座元件所特有的高度重复序列，尤其是最新的转座元件，它们与祖先序列的差异最小（对重建最有信息价值）。这对很多人来说是可以接受的，因为基因最重要的部分不是重复的，但对于转座元件爱好者来说，这是一个问题。ReAS是一种仅使用全基因组鸟枪法的未组装读段进行转座元件重建的新算法。针对粳稻的全基因组鸟枪法进行测试时，它被证明能够产生一个优于人工整理的已知祖先转座元件Repbase数据库的库。
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. Transposable elements (TEs) are a major component of the genomes of multicellular organisms. They are parasitic creatures that invade the genome, insert multiple copies of themselves, and then die. All we see now are the decayed remnants of their ancestral sequences. Reconstruction of these ancestral sequences can bring dead TEs back to life. Algorithms for detecting TEs compare present-day sequences to a library of ancestral sequences. Unknown to many, pervasive use of whole genome shotgun (WGS) methods in large-scale sequencing have made TE reconstructions increasingly problematic. To minimize assembly errors, WGS methods must reject the highly repetitive sequences that characterize most TEs, especially the most recent TEs, which are the least diverged from their ancestral sequences (and most informative for reconstruction). This is acceptable to many, because the most important parts of the genes are not repetitive, but for the TE aficionados, it is a problem. ReAS is a novel algorithm that does TE reconstruction using only the unassembled reads of a WGS. Tested against the WGS for japonica rice, it is shown to produce a library that is superior to the manually curated Repbase database of known ancestral TEs.
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DOI：
10.1073/pnas.97.13.7002
发表时间：
2000-06-20
影响因子：
11.1
作者：
Fedoroff, N
通讯作者：
Fedoroff, N
影响因子：
64.8
作者：
Sasaki, T;Matsumoto, T;Gojohori, T
通讯作者：
Gojohori, T
影响因子：
4
作者：
Smit, AFA
通讯作者：
Smit, AFA
影响因子：
4.2
作者：
Sanmiguel, P;Bennetzen, JL
通讯作者：
Bennetzen, JL
影响因子：
9.8
作者：
Yu J;Wang J;Lin W;Li S;Li H;Zhou J;Ni P;Dong W;Hu S;Zeng C;Zhang J;Zhang Y;Li R;Xu Z;Li S;Li X;Zheng H;Cong L;Lin L;Yin J;Geng J;Li G;Shi J;Liu J;Lv H;Li J;Wang J;Deng Y;Ran L;Shi X;Wang X;Wu Q;Li C;Ren X;Wang J;Wang X;Li D;Liu D;Zhang X;Ji Z;Zhao W;Sun Y;Zhang Z;Bao J;Han Y;Dong L;Ji J;Chen P;Wu S;Liu J;Xiao Y;Bu D;Tan J;Yang L;Ye C;Zhang J;Xu J;Zhou Y;Yu Y;Zhang B;Zhuang S;Wei H;Liu B;Lei M;Yu H;Li Y;Xu H;Wei S;He X;Fang L;Zhang Z;Zhang Y;Huang X;Su Z;Tong W;Li J;Tong Z;Li S;Ye J;Wang L;Fang L;Lei T;Chen C;Chen H;Xu Z;Li H;Huang H;Zhang F;Xu H;Li N;Zhao C;Li S;Dong L;Huang Y;Li L;Xi Y;Qi Q;Li W;Zhang B;Hu W;Zhang Y;Tian X;Jiao Y;Liang X;Jin J;Gao L;Zheng W;Hao B;Liu S;Wang W;Yuan L;Cao M;McDermott J;Samudrala R;Wang J;Wong GK;Yang H
通讯作者：
Yang H