Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes.
Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes.
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DOI：
10.1186/1471-2105-11-397
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发表时间：
2010-07-23
影响因子：
3
通讯作者：
Su Z
中科院分区：
文献类型：
--
作者：
Zhang S;Li S;Pham PT;Su Z
由于缺乏在基因组水平预测转录因子结合位点的准确和有效的计算方法，我们目前对测序的原核生物基因组中转录因子结合位点的了解非常有限。为了改变这种情况，我们最近开发了一种基于比较基因组学的算法GLECLUBS，用于从头开始预测目标基因组中的TFBS。尽管GLECLUBS已经取得了较高的目标基因组中TFBS的预测精度，但它仍然不足以应用于所有测序的原核基因组。在这里，我们设计了一种基于GLECLUBS的新算法，称为扩展GLECLUBS(EGLECLUBS)，用于同时预测一组相关原核生物基因组中的TFBs。当使用相同的参数设置对包括E.coliK12的一组γ蛋白细菌基因组、包括B.subtilis的一组固氮菌基因组和一组蓝藻基因组进行测试时，eGLECLUBS预测在提取的E.coliK12和B.subtilis的操纵子间序列中超过82%的已知TFBs。因为一个组中的每个基因组都被平等对待，所以该组中的每个基因组很可能都达到了类似的预测精度。我们开发了一种新的算法，用于在一组相关的原核生物基因组中对TFBS进行全基因组从头预测。该算法达到了与其前身GLECLUBS相同的精度和稳健性，但可以同时处理数十个基因组。
Our current understanding of transcription factor binding sites (TFBSs) in sequenced prokaryotic genomes is very limited due to the lack of an accurate and efficient computational method for the prediction of TFBSs at a genome scale. In an attempt to change this situation, we have recently developed a comparative genomics based algorithm called GLECLUBS for de novo genome-wide prediction of TFBSs in a target genome. Although GLECLUBS has achieved rather high prediction accuracy of TFBSs in a target genome, it is still not efficient enough to be applied to all the sequenced prokaryotic genomes. Here, we designed a new algorithm based on GLECLUBS called extended GLECLUBS (eGLECLUBS) for simultaneous prediction of TFBSs in a group of related prokaryotic genomes. When tested on a group of γ-proteobacterial genomes including E. coli K12, a group of firmicutes genomes including B. subtilis and a group of cyanobacterial genomes using the same parameter settings, eGLECLUBS predicts more than 82% of known TFBSs in extracted inter-operonic sequences in both E. coli K12 and B. subtilis. Because each genome in a group is equally treated, it is highly likely that similar prediction accuracy has been achieved for each genome in the group. We have developed a new algorithm for genome-wide de novo prediction of TFBSs in a group of related prokaryotic genomes. The algorithm has achieved the same level of accuracy and robustness as its predecessor GLECLUBS, but can work on dozens of genomes at the same time.
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DOI：
10.1142/s0219720003000162
发表时间：
2003-04-01
影响因子：
1
作者：
Olman, Victor;Xu, Dong;Xu, Ying
通讯作者：
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影响因子：
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作者：
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DOI：
10.1073/pnas.93.19.10268
发表时间：
1996-09-17
影响因子：
11.1
作者：
Mushegian, AR;Koonin, EV
通讯作者：
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影响因子：
14.9
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Gama-Castro S;Jiménez-Jacinto V;Peralta-Gil M;Santos-Zavaleta A;Peñaloza-Spinola MI;Contreras-Moreira B;Segura-Salazar J;Muñiz-Rascado L;Martínez-Flores I;Salgado H;Bonavides-Martínez C;Abreu-Goodger C;Rodríguez-Penagos C;Miranda-Ríos J;Morett E;Merino E;Huerta AM;Treviño-Quintanilla L;Collado-Vides J
通讯作者：
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影响因子：
14.9
作者：
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通讯作者：
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