Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences.
Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences.
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作者：
Edgar RC
预测 16S 核糖体 RNA (rRNA) 等标记基因序列的分类是微生物学的一项基本任务。大多数实验观察到的序列与权威命名的生物体的参考序列不同，这给预测方法带来了挑战。我使用身份交叉验证评估了几种算法的准确性，这是一种新的基准策略，它明确地模拟了查询序列与参考数据库中最近的条目之间的距离变化。当属预测的准确性在参考数据库的代表性身份范围（100%、99%、97%、95%和90%）上进行平均时，所有测试方法对当前流行的 16S rRNA V4 区域的准确性≤50%。研究发现，准确性随着身份的增加而迅速下降；例如，更好的方法被发现在 100% 同一性下 V4 属预测准确度为 ∼100%，但在 97% 同一性下为 ∼50%。身份和分类之间的关系被量化为具有给定成对身份的一对序列所共享的最低等级的概率。对于 V4 区域，95% 的同一性被发现是一个分类学高度模糊的模糊区域，因为序列对之间的最低共享等级是属、科、目或纲的概率大致相等。
Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA) is a fundamental task in microbiology. Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction methods. I assessed the accuracy of several algorithms using cross-validation by identity, a new benchmark strategy which explicitly models the variation in distances between query sequences and the closest entry in a reference database. When the accuracy of genus predictions was averaged over a representative range of identities with the reference database (100%, 99%, 97%, 95% and 90%), all tested methods had ≤50% accuracy on the currently-popular V4 region of 16S rRNA. Accuracy was found to fall rapidly with identity; for example, better methods were found to have V4 genus prediction accuracy of ∼100% at 100% identity but ∼50% at 97% identity. The relationship between identity and taxonomy was quantified as the probability that a rank is the lowest shared by a pair of sequences with a given pair-wise identity. With the V4 region, 95% identity was found to be a twilight zone where taxonomy is highly ambiguous because the probabilities that the lowest shared rank between pairs of sequences is genus, family, order or class are approximately equal.
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影响因子：
3
作者：
Gao X;Lin H;Revanna K;Dong Q
通讯作者：
Dong Q
影响因子：
48
作者：
Callahan BJ;McMurdie PJ;Rosen MJ;Han AW;Johnson AJ;Holmes SP
通讯作者：
Holmes SP
影响因子：
5.8
作者：
Edgar, Robert C.
通讯作者：
Edgar, Robert C.
DOI：
10.1073/pnas.1000080107
发表时间：
2011-03-15
影响因子：
11.1
作者：
Caporaso, J. Gregory;Lauber, Christian L.;Knight, Rob
通讯作者：
Knight, Rob
影响因子：
4.4
作者：
Kozich, James J.;Westcott, Sarah L.;Schloss, Patrick D.
通讯作者：
Schloss, Patrick D.