A k-mer scheme to predict piRNAs and characterize locust piRNAs.
A k-mer scheme to predict piRNAs and characterize locust piRNAs.
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预测 piRNA 和表征蝗虫 piRNA 的 k-mer 方案
DOI：
10.1093/bioinformatics/btr016
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发表时间：
2011-03-15
期刊：
影响因子：
--
通讯作者：
Kang L
中科院分区：
文献类型：
--
作者：
Zhang Y;Wang X;Kang L
动机：由于pirna在不同物种中缺乏保守的二级结构基序和序列同源性，鉴定非模式生物的piwi相互作用rna （pirna）是一个困难且尚未解决的问题。结果：本文提出了一种k-mer方案来识别piRNA序列，该方案依赖于大鼠、小鼠、人、果蝇和线虫五种模式物种的非piRNA和piRNA序列的训练集。与现有的基于位置特定碱基使用的“静态”方案相比，我们的新“动态”算法具有更好的性能，精度超过90%，灵敏度超过60%，并且在这些物种中进行了5倍交叉验证。为了验证其有效性，我们使用该算法基于603 607个深度测序的小RNA序列来识别迁徙蝗虫的pirna。共预测蝗虫pirna 87 536个，其中与已有蝗虫转座子匹配的pirna有4426个。描述了独居蝗虫和群居蝗虫的转录差异。我们还重新审视了pirna的位置特异性碱基使用，并发现了pirna末端的保守性。因此，我们开发的方法可以用于鉴定没有完整基因组序列的非模式生物的pirna。可用性：实现算法的web服务器和软件代码免费提供给学术界，网址为http://59.79.168.90/piRNA/index.php。补充信息：补充数据可在Bioinformatics在线获取。
Motivation: Identifying piwi-interacting RNAs (piRNAs) of non-model organisms is a difficult and unsolved problem because piRNAs lack conservative secondary structure motifs and sequence homology in different species. Results: In this article, a k-mer scheme is proposed to identify piRNA sequences, relying on the training sets from non-piRNA and piRNA sequences of five model species sequenced: rat, mouse, human, fruit fly and nematode. Compared with the existing ‘static’ scheme based on the position-specific base usage, our novel ‘dynamic’ algorithm performs much better with a precision of over 90% and a sensitivity of over 60%, and the precision is verified by 5-fold cross-validation in these species. To test its validity, we use the algorithm to identify piRNAs of the migratory locust based on 603 607 deep-sequenced small RNA sequences. Totally, 87 536 piRNAs of the locust are predicted, and 4426 of them matched with existing locust transposons. The transcriptional difference between solitary and gregarious locusts was described. We also revisit the position-specific base usage of piRNAs and find the conservation in the end of piRNAs. Therefore, the method we developed can be used to identify piRNAs of non-model organisms without complete genome sequences. Availability: The web server for implementing the algorithm and the software code are freely available to the academic community at http://59.79.168.90/piRNA/index.php. Contact: lkang@ioz.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
10.5
作者：
Watanabe, Toshiaki;Takeda, Atsushi;Imai, Hiroshi
通讯作者：
Imai, Hiroshi
蝗虫两个阶段小 RNA 转录组的表征和比较分析
影响因子：
12.3
作者：
Wei Y;Chen S;Yang P;Ma Z;Kang L
通讯作者：
Kang L
DOI：
10.1093/bioinformatics/btq020
发表时间：
2010-03-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Madera M;Calmus R;Thiltgen G;Karplus K;Gough J
通讯作者：
Gough J
DOI：
10.1073/pnas.91.26.12837
发表时间：
1994-12-20
影响因子：
11.1
作者：
KARLIN, S;LADUNGA, I;BLAISDELL, BE
通讯作者：
BLAISDELL, BE
影响因子：
64.5
作者：
Brennecke, Julius;Aravin, Alexei A.;Hannon, Gregory J.
通讯作者：
Hannon, Gregory J.