ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes.
ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes.
复制标题
DOI：
10.1186/1471-2105-7-9
复制
发表时间：
2006-01-10
影响因子：
3
通讯作者：
Zhang CT
中科院分区：
文献类型：
--
作者：
Guo FB;Zhang CT
病毒和噬菌体基因组注释需要使用高度精确的、基于免疫学的系统。用于在病毒和噬菌体基因组中发现基因的GeneMark系统具有一些基本缺点。本文提出了一种新的病毒和噬菌体基因发现方法，以提高注释的质量，特别是对新测序的基因组。ZCURVE_V系统已分别对979个病毒和212个噬菌体基因组进行了分析，获得了满意的结果。为了与现有的功能相似的软件GeneMark进行公平比较，共选择了30个尚未被GeneMark注释的病毒基因组进行测试。因此，两种系统的平均特异性很好地匹配，然而ZCURVE_V对较小病毒基因组（< 100 kb）的平均灵敏度高于GeneMark，较小病毒基因组构成迄今为止测序的病毒基因组的主要部分。此外，对于在测序的生物体中可能具有最低基因组GC含量的Amsacta moorei昆虫痘病毒的基因组，ZCURVE_V的准确性远远优于GeneMark，因为后者预测了数百个假阳性基因。ZCURVE_V还可用于分析研究充分的基因组，如HIV-1、HBV和SARS-CoV。因此，ZCURVE_V的性能通常优于GeneMark。最后，ZCURVE_V可以下载并在本地运行，特别是便于其使用，而GeneMark不可下载。基于上述比较，建议ZCURVE_V可作为新测序的病毒和噬菌体基因组的优选基因发现工具。然而，它也表明，这两个系统，ZCURVE_V和GeneMark的联合应用，导致更好的基因发现结果。系统ZCURVE_V可从以下网址免费获得：。ZCURVE_V可以作为病毒和噬菌体基因组的优选基因发现工具，特别是对于新测序的匿名病毒和噬菌体基因组。
It necessary to use highly accurate and statistics-based systems for viral and phage genome annotations. The GeneMark systems for gene-finding in virus and phage genomes suffer from some basic drawbacks. This paper puts forward an alternative approach for viral and phage gene-finding to improve the quality of annotations, particularly for newly sequenced genomes. The new system ZCURVE_V has been run for 979 viral and 212 phage genomes, respectively, and satisfactory results are obtained. To have a fair comparison with the currently available software of similar function, GeneMark, a total of 30 viral genomes that have not been annotated by GeneMark are selected to be tested. Consequently, the average specificity of both systems is well matched, however the average sensitivity of ZCURVE_V for smaller viral genomes (< 100 kb), which constitute the main parts of viral genomes sequenced so far, is higher than that of GeneMark. Additionally, for the genome of Amsacta moorei entomopoxvirus, probably with the lowest genomic GC content among the sequenced organisms, the accuracy of ZCURVE_V is much better than that of GeneMark, because the later predicts hundreds of false-positive genes. ZCURVE_V is also used to analyze well-studied genomes, such as HIV-1, HBV and SARS-CoV. Accordingly, the performance of ZCURVE_V is generally better than that of GeneMark. Finally, ZCURVE_V may be downloaded and run locally, particularly facilitating its utilization, whereas GeneMark is not downloadable. Based on the above comparison, it is suggested that ZCURVE_V may serve as a preferred gene-finding tool for viral and phage genomes newly sequenced. However, it is also shown that the joint application of both systems, ZCURVE_V and GeneMark, leads to better gene-finding results. The system ZCURVE_V is freely available at: . ZCURVE_V may serve as a preferred gene-finding tool used for viral and phage genomes, especially for anonymous viral and phage genomes newly sequenced.
登录
查看更多内容
影响因子：
5.6
作者：
TRIFONOV, EN
通讯作者：
TRIFONOV, EN
DOI：
10.1016/s0006-291x(03)01192-6
发表时间：
2003-07-25
影响因子：
3.1
作者：
Chen LL;Ou HY;Zhang R;Zhang CT
通讯作者：
Zhang CT
影响因子：
14.9
作者：
Besemer, J;Lomsadze, A;Borodovsky, M
通讯作者：
Borodovsky, M
影响因子：
14.9
作者：
Guo, FB;Ou, HY;Zhang, CT
通讯作者：
Zhang, CT
影响因子：
14.9
作者：
Besemer, J;Borodovsky, M
通讯作者：
Borodovsky, M