TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach.
TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach.
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DOI：
10.1186/1471-2105-10-56
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发表时间：
2009-02-11
影响因子：
3
通讯作者：
Nattkemper TW
中科院分区：
文献类型：
--
作者：
Diaz NN;Krause L;Goesmann A;Niehaus K;Nattkemper TW
宏基因组学，或对从环境中分离出来的微生物的集体基因组（宏基因组）进行测序和分析，有望直接接触到“不可培养的大多数”。这一新兴领域为我们对整个生命世界的理解奠定了坚实的基础。然而，分类分类是元基因组学数据集分析中的一个重要问题，至今仍未得到解决。我们提出了一种新的策略来预测环境基因组片段的分类起源。该分类器将k近邻的思想与基于核的学习策略相结合。我们的新策略使用留一交叉验证策略对来自373个完全测序的基因组的可变长度片段（800 bp - 50 Kbp）进行了广泛的评估。TACOA能够对长度为800 bp和1 Kbp的基因组片段进行分类，准确率很高，直到rank class。对于长度≥3 Kbp的片段，可以在更深的分类等级（目和属）上进行准确的预测。值得注意的是，当一个片段的分类起源没有在参考集中表示时，TACOA也能产生可靠的结果，从而将这些片段分类到已知的更广泛的分类类别中，或者简单地称为“未知”。我们使用最近发表的63个完整基因组比较了TACOA与最新的内在分类器PhyloPythia的分类精度。对于长度为800 bp和1 Kbp的片段，TACOA在所有分类等级上的总体精度都高于PhyloPythia。对于所有片段长度，两种方法都获得了相当高的特异性结果，最高可达等级，并且还获得了低假阴性率。建立了一个准确的环境基因组片段多类分类器。TACOA可以高可靠性地预测短至800 bp的基因组片段的分类起源。该方法具有透明、快速、准确、参考集易于更新等优点。此外，与最新的分类器PhyloPythia相比，该方法具有竞争力，并且具有可以在本地安装并且参考集可以保持最新的优势。
Metagenomics, or the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment, promises direct access to the "unculturable majority". This emerging field offers the potential to lay solid basis on our understanding of the entire living world. However, the taxonomic classification is an essential task in the analysis of metagenomics data sets that it is still far from being solved. We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning. Our novel strategy was extensively evaluated using the leave-one-out cross validation strategy on fragments of variable length (800 bp – 50 Kbp) from 373 completely sequenced genomes. TACOA is able to classify genomic fragments of length 800 bp and 1 Kbp with high accuracy until rank class. For longer fragments ≥ 3 Kbp accurate predictions are made at even deeper taxonomic ranks (order and genus). Remarkably, TACOA also produces reliable results when the taxonomic origin of a fragment is not represented in the reference set, thus classifying such fragments to its known broader taxonomic class or simply as "unknown". We compared the classification accuracy of TACOA with the latest intrinsic classifier PhyloPythia using 63 recently published complete genomes. For fragments of length 800 bp and 1 Kbp the overall accuracy of TACOA is higher than that obtained by PhyloPythia at all taxonomic ranks. For all fragment lengths, both methods achieved comparable high specificity results up to rank class and low false negative rates are also obtained. An accurate multi-class taxonomic classifier was developed for environmental genomic fragments. TACOA can predict with high reliability the taxonomic origin of genomic fragments as short as 800 bp. The proposed method is transparent, fast, accurate and the reference set can be easily updated as newly sequenced genomes become available. Moreover, the method demonstrated to be competitive when compared to the most current classifier PhyloPythia and has the advantage that it can be locally installed and the reference set can be kept up-to-date.
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影响因子：
56.9
作者：
FLEISCHMANN, RD;ADAMS, MD;VENTER, JC
通讯作者：
VENTER, JC
影响因子：
4.4
作者：
Bohlin, Jon;Skjerve, Eystein;Ussery, David W.
通讯作者：
Ussery, David W.
影响因子：
22.7
作者：
SALTON, G;WONG, A;YANG, CS
通讯作者：
YANG, CS
影响因子：
12.3
作者：
Podell S;Gaasterland T
通讯作者：
Gaasterland T
影响因子：
3.2
作者：
Karlin, S;Mrazek, J;Campbell, AM
通讯作者：
Campbell, AM