SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences.
SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences.
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DOI：
10.1093/bioinformatics/bts544
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发表时间：
2012-11-15
期刊：
影响因子：
--
通讯作者：
Clark TG
中科院分区：
文献类型：
--
作者：
Coll F;Mallard K;Preston MD;Bentley S;Parkhill J;McNerney R;Martin N;Clark TG
摘要：Spoligotyping 是一种成熟的基因分型技术，基于结核病 (TB) 病原体结核分枝杆菌 (Mtb) 中存在的独特 DNA 序列。尽管测序技术的进步正在导致全基因组细菌表征，但已经对数以万计的分离株进行了 spoligotype 分析，从而提供了 Mtb 菌株多样性的全球视图。为了弥补这一差距，我们开发了 SpolPred，这是一种根据原始序列读数预测 spoligotype 的软件。我们的方法与实验和从头组装确定的 44 个 Mtb 分离株中的菌株类型进行了比较。几乎所有分离株的计算机模拟和实验结果都是相同的 (39/44)。然而，SpolPred 检测到了五种实验性错误的 spoligotype，并且比组装策略更准确、更快。将 SpolPred 应用于没有实验室数据的另外 7 个分离株，在使用单核苷酸多态性的系统发育分析中，得到了与相同实验类型聚类的类型。我们的结果证明了该工具的有用性及其在揭示实验局限性方面的作用。可用性和实施：SpolPred 用 C 语言编写，可从 www.pathogenseq.org/spolpred 获取。联系方式：francesc.coll@lshtm.ac.uk 补充信息：补充数据可在生物信息学在线获取。
Summary: Spoligotyping is a well-established genotyping technique based on the presence of unique DNA sequences in Mycobacterium tuberculosis (Mtb), the causal agent of tuberculosis disease (TB). Although advances in sequencing technologies are leading to whole-genome bacterial characterization, tens of thousands of isolates have been spoligotyped, giving a global view of Mtb strain diversity. To bridge the gap, we have developed SpolPred, a software to predict the spoligotype from raw sequence reads. Our approach is compared with experimentally and de novo assembly determined strain types in a set of 44 Mtb isolates. In silico and experimental results are identical for almost all isolates (39/44). However, SpolPred detected five experimentally false spoligotypes and was more accurate and faster than the assembling strategy. Application of SpolPred to an additional seven isolates with no laboratory data led to types that clustered with identical experimental types in a phylogenetic analysis using single-nucleotide polymorphisms. Our results demonstrate the usefulness of the tool and its role in revealing experimental limitations. Availability and implementation: SpolPred is written in C and is available from www.pathogenseq.org/spolpred. Contact: francesc.coll@lshtm.ac.uk Supplementary information: Supplementary data are available at Bioinformatics Online.
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影响因子：
3.7
作者：
Ioerger TR;Koo S;No EG;Chen X;Larsen MH;Jacobs WR Jr;Pillay M;Sturm AW;Sacchettini JC
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