DNA Base-Calling from a Nanopore Using a Viterbi Algorithm
DNA Base-Calling from a Nanopore Using a Viterbi Algorithm
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DOI：
10.1016/j.bpj.2012.04.009
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发表时间：
2012-05-16
影响因子：
3.4
通讯作者：
Aksimentiev, Aleksei
中科院分区：
文献类型：
--
作者：
Timp, Winston;Comer, Jeffrey;Aksimentiev, Aleksei
基于纳米孔的DNA测序是最有前途的第三代测序方法。与最先进的第二代方法相比，它具有上级读取长度、速度和样品要求。然而，碱基识别仍然存在很大的困难，因为与测量的信噪比相比，该技术的分辨率是有限的。在这里，我们展示了一种方法，解码3 bp分辨率的纳米孔电测量到DNA序列使用隐马尔可夫模型。该方法显示出巨大的准确性潜力（类似于98%），即使信噪比很差。
Nanopore-based DNA sequencing is the most promising third-generation sequencing method. It has superior read length, speed, and sample requirements compared with state-of-the-art second-generation methods. However, base-calling still presents substantial difficulty because the resolution of the technique is limited compared with the measured signal/noise ratio. Here we demonstrate a method to decode 3-bp-resolution nanopore electrical measurements into a DNA sequence using a Hidden Markov model. This method shows tremendous potential for accuracy (similar to 98%), even with a poor signal/noise ratio.