Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information
Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information
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DOI：
10.1093/nar/24.17.3439
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发表时间：
1996-09-01
影响因子：
14.9
通讯作者：
Brunak, S
中科院分区：
文献类型：
--
作者：
Hebsgaard, SM;Korning, PG;Brunak, S
人工神经网络已与基于规则的系统相结合，以预测DICOT植物拟南芥中的内含子剪接位点，这是一个两步的预测方案，其中编码电位的全球预测调节了剪接站点的局部预测，该临界水平是根据剪接站点置信值，预测分数，编码上下文和潜在剪接站点之间的距离而精致的规则。在这种方法中，剪接站点的预测以非本地方式相互影响，合并的方法大大降低了通常困扰剪接位点预测的大量假阳性剪接位点，对网络在网络中的分析进行分析该方法的第一步揭示了一个以前未知的特征，这是外显子5'末端的频繁的t缩延长，此处介绍的方法已与此相比其他三种方法，Genefinder，Genemark和Grail，总的来说，此处介绍的方法更好，我们表明，新方法能够在果冻鱼绿色荧光蛋白的编码顺序中找到供体位点，正是在A.thaliana转化体中观察到的位置，还提出了对剪接基因的预测，以及其他双子骨，单子叶植物和藻类的基因的例子，该方法已通过电子邮件（netplantgene@cbs.dtu.dk）或http://www.cbs.dtu.dtu.dk/netplantgene.html提供。
Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana, A two step prediction scheme, where a global prediction of the coding potential regulates a cutoff level for a local prediction of splice sites, is refined by rules based on splice site confidence values, prediction scores, coding context and distances between potential splice sites. In this approach, the prediction of splice sites mutually affect each other in a non-local manner, The combined approach drastically reduces the large amount of false positive splice sites normally haunting splice site prediction, An analysis of the errors made by the networks in the first step of the method revealed a previously unknown feature, a frequent T-tract prolongation containing cryptic acceptor sites in the 5' end of exons, The method presented here has been compared with three other approaches, GeneFinder, GeneMark and Grail, Overall the method presented here is an order of magnitude better, We show that the new method is able to find a donor site in the coding sequence for the jelly fish Green Fluorescent Protein, exactly at the position that was experimentally observed in A.thaliana transformants, Predictions for alternatively spliced genes are also presented, together with examples of genes from other dicots, monocots and algae, The method has been made available through electronic mail (NetPlantGene@cbs.dtu.dk), or the WWW at http://www.cbs.dtu.dk/NetPlantGene.html