Computational Biology Research Center, AIST, Tokyo, Japan.
Proteomics. 2010 Nov;10(22):3970-83. doi: 10.1002/pmic.201000274. Epub 2010 Nov 2.
Since the proposal of the signal hypothesis on protein subcellular sorting, a number of computational analyses have been performed in this field. A typical example is the development of prediction algorithms for the subcellular localization sites of input protein sequences. In this review, we mainly focus on the biological grounds of the prediction methods rather than the algorithmic issues because we believe the former will be more fruitful for future development. Recent advances on the study of protein sorting signals will hopefully be incorporated into future prediction methods. Unfortunately, many of the state-of-the-art methods are published without sufficient objective tests. In fact, a simple test employed in this article shows that the performance of specifically developed predictors is not significantly better than that of a homology search. We suspect that this is a general problem associated with the interpretation of genome sequences, which have evolved through gene duplication and speciation.
自从提出蛋白质亚细胞分拣的信号假说以来，该领域已经进行了许多计算分析。一个典型的例子是开发用于输入蛋白质序列亚细胞定位的预测算法。在这篇综述中，我们主要关注预测方法的生物学基础，而不是算法问题，因为我们相信前者将对未来的发展更有成效。希望将蛋白质分拣信号研究的最新进展纳入未来的预测方法中。不幸的是，许多最先进的方法在没有充分的客观测试的情况下发布。事实上，本文中采用的一个简单测试表明，专门开发的预测器的性能并不明显优于同源搜索。我们怀疑这是一个与基因组序列解释相关的普遍问题，这些序列通过基因复制和物种形成而进化。
