Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA
Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA
复制标题
DOI：
10.1093/nar/26.20.4748
复制
发表时间：
1998-10-15
影响因子：
14.9
通讯作者：
Kleffe, J
中科院分区：
文献类型：
--
作者：
Brendel, V;Kleffe, J
序列检查的剪接位点选择和效率的预测具有基本兴趣（测试必要序列特征的当前知识）和实际重要性（基因组注释，突变或转基因生物的设计），在植物中，主要的变量影响剪接位点的选择和剪接位点的选择和效率包括与扩展的剪接位点共识的匹配程度以及U-和G+C-组合的局部梯度（内含子是U-Rich和Exons G+C-Rich），我们提出了一种新颖的方法来剪接位点预测，该方法是针对玉米和拟南芥的训练，该方法通过同时考虑三个变量：内在的剪接站点强度，局部最佳性和相对于整体剪接模式预测的拟合，从而扩展了我们以前的算法。我们表明，该方法大大提高了预测特异性，而不会损害基因预测算法所需的高度灵敏度。为拟南芥中的应用说明了对基因识别的应用，并表明成功的方法必须以非平凡的方式结合剪接站点的评分，编码潜力和相似性与潜在同源物。 SplicePredictor程序的www版本可在http：/gnomic.stanford.edu/volker/splicepredictor.html/。
Prediction of splice site selection and efficiency from sequence inspection is of fundamental interest (testing the current knowledge of requisite sequence features) and practical importance (genome annotation, design of mutant or transgenic organisms), In plants, the dominant variables affecting splice site selection and efficiency include the degree of matching to the extended splice site consensus and the local gradient of U- and G+C-composition (introns being U-rich and exons G+C-rich), We present a novel method for splice site prediction, which was particularly trained for maize and Arabidopsis thaliana, The method extends our previous algorithm based on logitlinear models by considering three variables simultaneously: intrinsic splice site strength, local optimality and fit with respect to the overall splice pattern prediction. We show that the method considerably improves prediction specificity without compromising the high degree of sensitivity required in gene prediction algorithms. Applications to gene identification are illustrated for Arabidopsis and suggest that successful methods must combine scoring for splice sites, coding potential and similarity with potential homologs in non-trivial ways. A WWW version of the SplicePredictor program is available at http:/gnomic.stanford.edu/ volker/SplicePredictor.html/.