GeneID in Drosophila
GeneID in Drosophila
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DOI：
10.1101/gr.10.4.511
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发表时间：
2000-04-01
期刊：
影响因子：
7
通讯作者：
Guigó, R
中科院分区：
文献类型：
--
作者：
Parra, G;Blanco, E;Guigó, R
GeneID是一个预测匿名基因组序列中的基因的程序，该基因组序列设计有层次结构。在第一步中，使用位置权重矩阵（PWM）预测剪接位点以及起始和终止密码子，并沿序列进行沿着评分。在第二步中，从位点构建外显子。外显子的评分是定义位点的评分之和，加上编码DNA的马尔可夫模型的对数似然比。在最后一步中，从预测的外显子集合中，组装基因结构，最大化组装的外显子的得分之和。本文描述了果蝇DNA编码位点的PWM的获得和编码DNA的Markov模型。我们还比较了其他模型的编码DNA与马尔可夫模型。最后，我们提出并讨论了GeneID用于预测Adh区域中的基因时所获得的结果。这些结果表明，GeneID预测的准确性目前与其他现有工具相比，但GeneID在速度和内存使用方面可能更有效。GeneID可在http://wwwl.imim.es/similar上向eblanco/Geneld提供。
GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the First step, splice sites, and start and stop codons are predicted and scored along the sequence using position weight matrices (PWMs). In the second step, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the log-likelihood ratio of a Markov model for coding DNA. In the last step, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. In this paper we describe the obtention of PWMs for sites, and the Markov model of coding DNA in Drosophila melanogaster. We also compare other models of coding DNA with the Markov model. Finally, we present and discuss the results obtained when GeneID is used to predict genes in the Adh region. These results show that the accuracy of GeneID predictions compares currently with that of other existing tools but that GeneID is likely to be more efficient in terms of speed and memory usage. GeneID is available at http://wwwl.imim.es/similar to eblanco/Geneld.