PREDICTING POL-II PROMOTER SEQUENCES USING TRANSCRIPTION FACTOR-BINDING SITES
PREDICTING POL-II PROMOTER SEQUENCES USING TRANSCRIPTION FACTOR-BINDING SITES
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DOI：
10.1006/jmbi.1995.0349
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发表时间：
1995-06-23
影响因子：
5.6
通讯作者：
PRESTRIDGE, DS
中科院分区：
文献类型：
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作者：
PRESTRIDGE, DS
一个计算机程序，启动子扫描，已经开发出识别高百分比的Pol II启动子序列，而只允许一个小的假阳性率。167个灵长类动物Pol II启动子序列来自真核生物启动子数据库，999个灵长类动物非启动子序列来自GenBank序列数据库。对Ghosh转录因子数据库中列出的每个独特的哺乳动物转录因子结合位点的启动子序列和非启动子序列进行比较密度分析。然后使用这些结合位点的密度来得出启动子与非启动子序列中每个转录元件的密度之比。然后将所有结合位点的组合个体密度比共同用于构建称为启动子识别谱的评分谱。然后，启动子扫描程序使用该配置文件与加权矩阵一起对TATA盒进行评分，以测试启动子序列的预测以及计算机程序区分它们与非启动子序列的能力。当设定启动子截断分数，使70%的启动子被程序正确识别时，在非启动子序列集中观察到假阳性率约为1/5600个碱基。目前正在开发PROMOTER SCAN以供公众分发。
A computer program, PROMOTER SCAN, has been developed to recognize a high percentage of Pol II promoter sequences while allowing only a small rate of false positives. A total of 167 primate Pol II promoter sequences, obtained from the Eukaryotic Promoter Database, and 999 primate non-promoter sequences, obtained from the GenBank sequence databank, were used in the analysis. Both promoter and non-promoter sequences were analyzed for the comparative density of each unique mammalian transcription factor binding site listed in the Ghosh Transcription Factor Database. The density of each of these binding sites was then used to derive a ratio of density of each transcriptional element in promoter compared to non-promoter sequences. The combined individual density ratios of all binding sites were then collectively used to build a scoring profile called the Promoter Recognition Profile. This profile, used in combination with a weighted matrix for scoring a TATA box, was then used by the PROMOTER SCAN program to test the prediction of promoter sequences and the ability of the computer program to discriminate them from non-promoter sequences. When the promoter cutoff score was set so that 70% of promoters were recognized correctly by the program, a false positive rate of about 1/5600 bases was observed in the non-promoter sequence set. PROMOTER SCAN is now being developed for public distribution.