TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.
TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.
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DOI：
10.3389/fpls.2012.00005
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发表时间：
2012
影响因子：
5.6
通讯作者：
Feuillet C
中科院分区：
文献类型：
--
作者：
Leroy P;Guilhot N;Sakai H;Bernard A;Choulet F;Theil S;Reboux S;Amano N;Flutre T;Pelegrin C;Ohyanagi H;Seidel M;Giacomoni F;Reichstadt M;Alaux M;Gicquello E;Legeai F;Cerutti L;Numa H;Tanaka T;Mayer K;Itoh T;Quesneville H;Feuillet C
为了支持获得面包小麦基因组参考序列的国际努力，并为处理大型复杂基因组的植物社区提供通用，易于使用的在线自动化注释工具，我们开发了TriAnnot管道。它的模块化架构允许转座因子的注释和掩蔽，蛋白质编码基因的结构和功能注释，以及基于证据的质量索引，以及保守的非编码序列和分子标记的鉴定。TriAnnot流水线在712 CPU计算集群上并行化，可以在不到5天的时间内运行1 Gb序列注释。它可以通过Web界面进行小规模分析或通过服务器进行大规模注释。TriAnnot的性能进行了评估的敏感性，特异性和一般的健身使用精选的参考序列集从水稻和小麦。在不到8 h的时间内，TriAnnot能够预测水稻1号染色体3，748个CDS中的83%以上，适应度为67.4%。在小麦3B染色体的12个参考Mb大小的重叠群上，TriAnnot预测和注释了93.3%的基因，其中54%与参考注释完全一致。它还允许基于新的生物学证据对12个基因进行管理，将完美基因预测的百分比提高到63%。TriAnnot系统地显示出比其他未针对小麦进行改进的注释管道更高的适应度。由于TriAnnot易于应用于其他植物基因组的注释，它将成为未来大型复杂基因组注释的有用资源。
In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future.
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影响因子：
7
作者：
Curwen, V;Eyras, E;Clamp, M
通讯作者：
Clamp, M
DOI：
10.1073/pnas.0509473102
发表时间：
2005-12-27
影响因子：
11.1
作者：
Devos, KM;Ma, JX;Bennetzen, JL
通讯作者：
Bennetzen, JL
影响因子：
1
作者：
Feuillet, Catherine;Eversole, Kellye
通讯作者：
Eversole, Kellye
影响因子：
14.9
作者：
Letunic I;Doerks T;Bork P
通讯作者：
Bork P
DOI：
10.1093/dnares/dsq017
发表时间：
2010-10
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Amano N;Tanaka T;Numa H;Sakai H;Itoh T
通讯作者：
Itoh T