AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.
AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.
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DOI：
10.1186/gb-2006-7-s1-s11
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发表时间：
2006
期刊：
影响因子：
12.3
通讯作者：
Morgenstern, Burkhard
中科院分区：
文献类型：
--
作者：
Stanke, Mario;Tzvetkova, Ana;Morgenstern, Burkhard
存在大量针对人类基因组的基因预测程序。这些注释工具使用多种方法和数据源。在最近的ENCODE基因组注释评估项目（EGASP）中，一些最常用和最近开发的基因预测程序根据人类基因组的测试数据进行了系统评估和比较。 AUGUSTUS 是该项目中测试的工具之一。 AUGUSTUS 可以用作 ab initio 程序，即仅使用一个基因组序列作为输入信息的程序。此外，它能够将所研究的基因组序列的信息与来自各种信息源的外部提示结合起来。对于 EGASP，我们使用基因组序列比对以及表达序列标签 (EST) 和蛋白质序列比对作为额外的信息来源。在从头算程序的类别中，奥古斯特斯比任何其他从头算程序正确预测的基因明显更多。同时，它在所有从头算程序中预测了最少数量的假阳性基因和最少数量的假阳性外显子。当考虑到额外的外在数据（例如与 EST、蛋白质和/或基因组序列的比对）时，AUGUSTUS 的准确性可以进一步提高。事实证明，AUGUSTUS 是经过测试的工具中最准确的从头开始基因查找器。此外，它非常灵活，因为它可以同时考虑多个来源的信息。
A large number of gene prediction programs for the human genome exist. These annotation tools use a variety of methods and data sources. In the recent ENCODE genome annotation assessment project (EGASP), some of the most commonly used and recently developed gene-prediction programs were systematically evaluated and compared on test data from the human genome. AUGUSTUS was among the tools that were tested in this project. AUGUSTUS can be used as an ab initio program, that is, as a program that uses only one single genomic sequence as input information. In addition, it is able to combine information from the genomic sequence under study with external hints from various sources of information. For EGASP, we used genomic sequence alignments as well as alignments to expressed sequence tags (ESTs) and protein sequences as additional sources of information. Within the category of ab initio programs AUGUSTUS predicted significantly more genes correctly than any other ab initio program. At the same time it predicted the smallest number of false positive genes and the smallest number of false positive exons among all ab initio programs. The accuracy of AUGUSTUS could be further improved when additional extrinsic data, such as alignments to EST, protein and/or genomic sequences, was taken into account. AUGUSTUS turned out to be the most accurate ab initio gene finder among the tested tools. Moreover it is very flexible because it can take information from several sources simultaneously into consideration.
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影响因子：
5.8
作者：
Stanke, Mario;Waack, Stephan
通讯作者：
Waack, Stephan
影响因子：
7
作者：
Guigó, R;Agarwal, P;Fickett, JW
通讯作者：
Fickett, JW
影响因子：
14.9
作者：
Stanke M;Keller O;Gunduz I;Hayes A;Waack S;Morgenstern B
通讯作者：
Morgenstern B
影响因子：
12.3
作者：
Guigó R;Flicek P;Abril JF;Reymond A;Lagarde J;Denoeud F;Antonarakis S;Ashburner M;Bajic VB;Birney E;Castelo R;Eyras E;Ucla C;Gingeras TR;Harrow J;Hubbard T;Lewis SE;Reese MG
通讯作者：
Reese MG
影响因子：
5.8
作者：
Morgenstern, B
通讯作者：
Morgenstern, B