ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes
ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes
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DOI：
10.1093/nar/gkg254
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发表时间：
2003-03-15
影响因子：
14.9
通讯作者：
Zhang, CT
中科院分区：
文献类型：
--
作者：
Guo, FB;Ou, HY;Zhang, CT
提出了一个新的系统ZCURVE 1.0，用于在细菌和古细菌基因组中寻找蛋白编码基因.该算法基于DNA序列的Z曲线表示，通过考虑三个密码子位置上碱基的频率，强调蛋白质编码基因的全局统计特征。在ZCURVE 1.0中，由于仅使用33个参数来表征编码序列，因此它更好地考虑了典型和非典型情况，而在基于马尔可夫模型的方法中，例如Glimmer 2.02，训练了数千个参数，这可能导致适应性较差。为了比较新系统与Glimmer 2.02的性能，分别对Glimmer系统未注释的18个基因组运行两个系统。同时对两种系统预测功能已知基因的结果进行了比较。因此，两个系统的平均准确度很好地匹配;然而，ZCURVE 1.0具有更准确的基因起始预测，更低的额外预测率和更高的水平转移基因的预测准确度。结果表明，两个系统的联合应用大大提高了基因发现的结果。对于一个典型的基因组，例如大肠杆菌，系统ZCURVE 1.0在奔腾III 866 PC上不需要任何人为干预的情况下需要大约2分钟。系统ZCURVE 1.0可在http：//tubic上免费获得。tju.edu.cn/Zcurve_B/.
A new system, ZCURVE 1.0, for finding protein- coding genes in bacterial and archaeal genomes has been proposed. The current algorithm, which is based on the Z curve representation of the DNA sequences, lays stress on the global statistical features of protein-coding genes by taking the frequencies of bases at three codon positions into account. In ZCURVE 1.0, since only 33 parameters are used to characterize the coding sequences, it gives better consideration to both typical and atypical cases, whereas in Markov-model-based methods, e.g. Glimmer 2.02, thousands of parameters are trained, which may result in less adaptability. To compare the performance of the new system with that of Glimmer 2.02, both systems were run, respectively, for 18 genomes not annotated by the Glimmer system. Comparisons were also performed for predicting some function-known genes by both systems. Consequently, the average accuracy of both systems is well matched; however, ZCURVE 1.0 has more accurate gene start prediction, lower additional prediction rate and higher accuracy for the prediction of horizontally transferred genes. It is shown that the joint applications of both systems greatly improve gene-finding results. For a typical genome, e.g. Escherichia coli, the system ZCURVE 1.0 takes similar to2 min on a Pentium III 866 PC without any human intervention. The system ZCURVE 1.0 is freely available at: http://tubic. tju.edu.cn/Zcurve_B/.