VariantClassifier: A hierarchical variant classifier for annotated genomes.
VariantClassifier: A hierarchical variant classifier for annotated genomes.
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DOI：
10.1186/1756-0500-3-191
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发表时间：
2010-07-13
影响因子：
1.8
通讯作者：
Stockwell TB
中科院分区：
文献类型：
--
作者：
Li K;Stockwell TB
高通量DNA测序已经产生了大量封闭的和注释良好的基因组。随着全基因组测序和组装的重点转向重测序，变异数据变得更容易获得，大量的多态性被检测到。一个易于使用的工具来快速评估这些发现的变异的潜在重要性变得越来越重要。用Perl编写的VariantClassifier接收多态性和基因组注释的列表，并为每个变体生成分层结构的分类。根据可用的注释，VariantClassifier可以将每个多态性分配给各种各样的特征类型，例如基因间或基因;上游启动子区、内含子区、外显子区或下游转录物区; 5'剪接位点或3'剪接位点; 5'非翻译区（UTR）、3' UTR或编码序列（CDS）;受影响的蛋白质结构域;取代、插入或缺失;同义或非同义;保守或不保守;和移码或氨基酸插入或缺失（插入缺失）。如果适用，还预测截短或改变的蛋白质序列。对于在Ensembl保存注释的微生物，还提供了用于下载必要注释的软件应用程序，尽管分类器将通过替代方法提供适当格式的注释来运行。自从VariantClassifier实现以来，我们已经在多个项目中使用了它，以快速评估多个基因组上的数十万个变异，并收到了将该工具投入使用的请求。该项目的网址是：http://www.jcvi.org/cms/research/projects/variantclassifier。
High-throughput DNA sequencing has produced a large number of closed and well annotated genomes. As the focus from whole genome sequencing and assembly moves towards resequencing, variant data is becoming more accessible and large quantities of polymorphisms are being detected. An easy-to-use tool for quickly assessing the potential importance of these discovered variants becomes ever important. Written in Perl, the VariantClassifier receives a list of polymorphisms and genome annotation, and generates a hierarchically-structured classification for each variant. Depending on the available annotation, the VariantClassifier may assign each polymorphism to a large variety of feature types, such as intergenic or genic; upstream promoter region, intronic region, exonic region or downstream transcript region; 5' splice site or 3' splice site; 5' untranslated region (UTR), 3' UTR or coding sequence (CDS); impacted protein domain; substitution, insertion or deletion; synonymous or non-synonymous; conserved or unconserved; and frameshift or amino acid insertion or deletion (indel). If applicable, the truncated or altered protein sequence is also predicted. For organisms with annotation maintained at Ensembl, a software application for downloading the necessary annotation is also provided, although the classifier will function with properly formatted annotation provided through alternative means. We have utilized the VariantClassifier for several projects since its implementation to quickly assess hundreds of thousands of variations on several genomes and have received requests to make the tool publically available. The project website can be found at: http://www.jcvi.org/cms/research/projects/variantclassifier.