nGASP--the nematode genome annotation assessment project.
nGASP--the nematode genome annotation assessment project.
复制标题
DOI：
10.1186/1471-2105-9-549
复制
发表时间：
2008-12-19
影响因子：
3
通讯作者：
Stein LD
中科院分区：
文献类型：
--
作者：
Coghlan A;Fiedler TJ;McKay SJ;Flicek P;Harris TW;Blasiar D;nGASP Consortium;Stein LD
虽然秀丽隐杆线虫的基因组被广泛注释，但相对较少的信息可用于其他秀丽隐杆线虫物种。线虫基因组注释评估项目（nematode genome annotation assessment project, nGASP）旨在客观评估线虫蛋白质编码基因预测软件的准确性，并将此知识应用于另外4种隐杆线虫和其他线虫的基因组注释。全球17个研究小组参与了nGASP，并提交了47个预测集，涵盖10 Mb的秀丽隐杆线虫基因组。将预测结果与参考基因集进行比较，这些参考基因集由来自WormBase的已确认或人工整理的基因模型组成。最准确的基因查找器是“组合”算法，它利用转录物和蛋白质比对以及多基因组比对，以及来自其他基因查找器的基因预测。使用est、mrna和蛋白质排列的基因发现者排在第二位。使用多基因组比对的基因寻找者和从头开始的基因寻找者并列第三。组合子的中位基因水平敏感性为78%，特异性为42%，这与人类基因组中组合子的准确性几乎相同。具有异常六聚体含量外显子的线虫基因，以及具有异常多外显子、短外显子、长内含子、弱翻译起始信号、弱剪接位点或保守性差的同源基因，对基因寻找者构成了最大的困难。本实验建立了隐杆线虫基因组基因预测精度的基线，并指导了隐杆线虫和其他线虫物种新测序基因组注释中基因发现者的选择。我们利用一些表现最好的基因寻找者为C. briggsae、C. remanei、C. brenneri、C. japonica和Brugia malayi创建了新的基因集。
While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets across 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with unusually many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs posed the greatest difficulty for gene-finders. This experiment establishes a baseline of gene prediction accuracy in Caenorhabditis genomes, and has guided the choice of gene-finders for the annotation of newly sequenced genomes of Caenorhabditis and other nematode species. We have created new gene sets for C. briggsae, C. remanei, C. brenneri, C. japonica, and Brugia malayi using some of the best-performing gene-finders.
登录
查看更多内容
FlyBase：十几个基因组。
影响因子：
14.9
作者：
Crosby MA;Goodman JL;Strelets VB;Zhang P;Gelbart WM;FlyBase Consortium
通讯作者：
FlyBase Consortium
TreeFam：动物基因家族系统发育树的精选数据库
影响因子：
14.9
作者：
Li, Heng;Coghlan, Avril;Ruan, Jue;Coin, Lachlan James;Heriche, Jean-Karim;Osmotherly, Lara;Li, Ruiqiang;Liu, Tao;Zhang, Zhang;Bolund, Lars;Wong, Gane Ka-Shu;Zheng, Weimou;Dehal, Paramvir;Wang, Jun;Durbin, Richard
通讯作者：
Durbin, Richard
影响因子：
7
作者：
Reese, MG;Hartzell, G;Lewis, SE
通讯作者：
Lewis, SE
影响因子：
3
作者：
Foissac S;Schiex T
通讯作者：
Schiex T
影响因子：
5.8
作者：
Liu, Qian;Mackey, Aaron J.;Pereira, Fernando C. N.
通讯作者：
Pereira, Fernando C. N.