SNAP: predict effect of non-synonymous polymorphisms on function.
SNAP: predict effect of non-synonymous polymorphisms on function.
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DOI：
10.1093/nar/gkm238
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发表时间：
2007
影响因子：
14.9
通讯作者：
Rost B
中科院分区：
文献类型：
--
作者：
Bromberg Y;Rost B
许多遗传变异是单核苷酸多态性（SNP）。如果所得的点突变蛋白在功能上与野生型不可区分，则非同义SNP是“中性的”，否则是“非中性的"。鉴定非中性取代的能力可以显著帮助靶向引起有害突变的疾病，以及增加特定表型适应性的SNP。在这里，我们引入了全面的数据集来评估预测SNP效应的方法的性能。沿着我们介绍了SNAP（筛选不可接受的多态性），一种基于神经网络的方法，用于预测非同义SNP的功能效应。SNAP仅需要序列信息作为输入，但如果可用，则受益于功能和结构注释。在对超过80000个突变体的交叉验证测试中，SNAP以77%的准确度鉴定了80%的非中性取代，以80%的准确度鉴定了76%的中性取代。这对其他方法来说是一个重要的改进;对于现有方法不同意的突变体，改进幅度上升到十个百分点以上。可能更重要的是，SNAP为每个预测的可靠性引入了一个校准良好的衡量标准。这一措施将使用户能够专注于最准确的预测和/或最严重的影响。可在http://www.rostlab.org/services/SNAP上获得
Many genetic variations are single nucleotide polymorphisms (SNPs). Non-synonymous SNPs are ‘neutral’ if the resulting point-mutated protein is not functionally discernible from the wild type and ‘non-neutral’ otherwise. The ability to identify non-neutral substitutions could significantly aid targeting disease causing detrimental mutations, as well as SNPs that increase the fitness of particular phenotypes. Here, we introduced comprehensive data sets to assess the performance of methods that predict SNP effects. Along we introduced SNAP (screening for non-acceptable polymorphisms), a neural network-based method for the prediction of the functional effects of non-synonymous SNPs. SNAP needs only sequence information as input, but benefits from functional and structural annotations, if available. In a cross-validation test on over 80 000 mutants, SNAP identified 80% of the non-neutral substitutions at 77% accuracy and 76% of the neutral substitutions at 80% accuracy. This constituted an important improvement over other methods; the improvement rose to over ten percentage points for mutants for which existing methods disagreed. Possibly even more importantly SNAP introduced a well-calibrated measure for the reliability of each prediction. This measure will allow users to focus on the most accurate predictions and/or the most severe effects. Available at http://www.rostlab.org/services/SNAP
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影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
影响因子：
3.5
作者：
KIDOKORO, S;MIKI, Y;OOE, S
通讯作者：
OOE, S
影响因子：
64.8
作者：
LOEB, DD;SWANSTROM, R;HUTCHISON, CA
通讯作者：
HUTCHISON, CA
影响因子：
4.5
作者：
Liu J;Gough J;Rost B
通讯作者：
Rost B
影响因子：
14.9
作者：
Bairoch, A;Apweiler, R
通讯作者：
Apweiler, R