基于 Viterbi 算法的纳米孔 DNA 碱基读取。
DNA base-calling from a nanopore using a Viterbi algorithm.
出版信息
Biophys J. 2012 May 16;102(10):L37-9. doi: 10.1016/j.bpj.2012.04.009. Epub 2012 May 15.
Abstract
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 (~98%), even with a poor signal/noise ratio.
摘要
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，它具有优越的读取长度、速度和样品要求。然而，碱基调用仍然存在很大的困难，因为与测量的信号/噪声比相比，该技术的分辨率有限。在这里，我们展示了一种使用隐马尔可夫模型将 3 个碱基分辨率的纳米孔电测量结果解码为 DNA 序列的方法。即使在信噪比较差的情况下，该方法也具有很高的准确性（~98%）。
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