Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
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DOI：
10.1038/nprot.2009.86
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发表时间：
2009-01-01
期刊：
影响因子：
14.8
通讯作者：
Ng, Pauline C.
中科院分区：
文献类型：
--
作者：
Kumar, Prateek;Henikoff, Steven;Ng, Pauline C.
遗传突变对表型的影响在遗传学中具有重大兴趣。在蛋白质序列中引起单个氨基酸取代（AA）的遗传突变的类型称为非同义单核苷酸多态性（NSSNP）。 NSSNP可能会影响蛋白质的功能，然后改变载体的表型。该协议描述了在预测AAS是否影响蛋白质功能时使用“不耐受的分类耐受性”（SIFT）算法的使用。为了评估替代的效果，SIFT假设蛋白质序列中的重要位置在整个进化过程中都得到了保守，因此在这些位置的替代可能会影响蛋白质功能。因此，通过使用序列同源性，SIFT预测了蛋白质序列中每个位置的所有可能取代的影响。该协议通常需要5-20分钟，具体取决于输入。 SIFT可作为在线工具（http://sift.jcvi.org）提供。
The effect of genetic mutation on phenotype is of significant interest in genetics. The type of genetic mutation that causes a single amino acid substitution (AAS) in a protein sequence is called a non-synonymous single nucleotide polymorphism (nsSNP). An nsSNP could potentially affect the function of the protein, subsequently altering the carrier's phenotype. This protocol describes the use of the 'Sorting Tolerant From Intolerant' (SIFT) algorithm in predicting whether an AAS affects protein function. To assess the effect of a substitution, SIFT assumes that important positions in a protein sequence have been conserved throughout evolution and therefore substitutions at these positions may affect protein function. Thus, by using sequence homology, SIFT predicts the effects of all possible substitutions at each position in the protein sequence. The protocol typically takes 5-20 min, depending on the input. SIFT is available as an online tool (http://sift.jcvi.org).