metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella.
metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella.
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DOI：
10.1093/nar/gki285
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发表时间：
2005
影响因子：
14.9
通讯作者：
Westhead DR
中科院分区：
文献类型：
--
作者：
Pinney JW;Shirley MW;McConkey GA;Westhead DR
代谢搜索和重建套件 (metaSHARK) 是一种全新的全自动软件包，用于检测未注释的基因组数据中的酶编码基因，并在周围代谢网络的背景下可视化它们。基因检测包 (SHARKhunt) 在 Linux 系统上运行，仅需要一组原始 DNA 序列（基因组、表达序列标签和/或基因组调查序列）作为输入。其输出可以上传到我们基于网络的可视化工具（SHARKview），用于探索和比较来自不同生物体的数据。我们首先通过将原始恶性疟原虫基因组的结果与 PlasmoDB 和 PlasmoCyc 网站上提供的手动注释进行比较来展示该软件的实用性。然后，我们将 SHARKhunt 应用于球虫寄生虫艾美耳球虫的未注释基因组序列，并观察到，在 E 值截止值为 10−20 时，与最近使用翻译的开放阅读框序列的注释包相比，我们的软件对酶功能进行了 142 个额外断言。通过以 0.5× 至 7.5× 的估计覆盖度分析 E.tenella 基因组的组装，研究了该软件应对低水平序列覆盖度的能力。最后，作为如何使用 metaSHARK 评估特定代谢途径的基因组证据的一个例子，我们提出了一项关于恶性疟原虫和球虫辅酶 A 生物合成的研究。
The metabolic SearcH And Reconstruction Kit (metaSHARK) is a new fully automated software package for the detection of enzyme-encoding genes within unannotated genome data and their visualization in the context of the surrounding metabolic network. The gene detection package (SHARKhunt) runs on a Linux system and requires only a set of raw DNA sequences (genomic, expressed sequence tag and/or genome survey sequence) as input. Its output may be uploaded to our web-based visualization tool (SHARKview) for exploring and comparing data from different organisms. We first demonstrate the utility of the software by comparing its results for the raw Plasmodium falciparum genome with the manual annotations available at the PlasmoDB and PlasmoCyc websites. We then apply SHARKhunt to the unannotated genome sequences of the coccidian parasite Eimeria tenella and observe that, at an E-value cut-off of 10−20, our software makes 142 additional assertions of enzymatic function compared with a recent annotation package working with translated open reading frame sequences. The ability of the software to cope with low levels of sequence coverage is investigated by analyzing assemblies of the E.tenella genome at estimated coverages from 0.5× to 7.5×. Lastly, as an example of how metaSHARK can be used to evaluate the genomic evidence for specific metabolic pathways, we present a study of coenzyme A biosynthesis in P.falciparum and E.tenella.
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影响因子：
7
作者：
Bono, H;Ogata, H;Kanehisa, M
通讯作者：
Kanehisa, M
DOI：
10.1111/j.1550-7408.1967.tb01985.x
发表时间：
1967-01-01
期刊：
JOURNAL OF PROTOZOOLOGY
影响因子：
--
作者：
BENNETT, TP;TRAGER, W
通讯作者：
TRAGER, W
影响因子：
3.4
作者：
Jackson, Laurie K.;Phillips, Margaret A.
通讯作者：
Phillips, Margaret A.
影响因子：
4.8
作者：
Saliba, KJ;Horner, HA;Kirk, K
通讯作者：
Kirk, K
影响因子：
14.9
作者：
Claudel-Renard, C;Chevalet, C;Kahn, D
通讯作者：
Kahn, D