串联重复注释库。
TRAL: tandem repeat annotation library.
机构信息
Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wäde
Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland.
出版信息
Bioinformatics. 2015 Sep 15;31(18):3051-3. doi: 10.1093/bioinformatics/btv306. Epub 2015 May 18.
MOTIVATION
Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results.
RESULTS
We present TRAL, a tandem repeat annotation library that allows running and parsing of various detection outputs, clustering of redundant or overlapping annotations, several statistical frameworks for filtering false positive annotations, and importantly a tandem repeat annotation and refinement module based on circular profile hidden Markov models (cpHMMs). Using TRAL, we evaluated the performance of a multi-step tandem repeat annotation workflow on 547 085 sequences in UniProtKB/Swiss-Prot. The researcher can use these results to predict run-times for specific datasets, and to choose annotation complexity accordingly.
AVAILABILITY AND IMPLEMENTATION
TRAL is an open-source Python 3 library and is available, together with documentation and tutorials via http://www.vital-it.ch/software/tral.
CONTACT
动机
目前，已有超过 40 种序列串联重复检测器发布，提供了异构的、部分互补的、部分冲突的结果。
结果
我们提出了 TRAL，这是一个串联重复注释库，它允许运行和解析各种检测输出，对冗余或重叠的注释进行聚类，提供了几个用于过滤假阳性注释的统计框架，以及一个重要的基于循环轮廓隐马尔可夫模型（cpHMM）的串联重复注释和细化模块。使用 TRAL，我们在 UniProtKB/Swiss-Prot 中的 547085 条序列上评估了多步串联重复注释工作流程的性能。研究人员可以使用这些结果预测特定数据集的运行时间，并相应地选择注释的复杂性。
可用性和实现
TRAL 是一个开源的 Python 3 库，并通过 http://www.vital-it.ch/software/tral 提供文档和教程。
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