Enrich: software for analysis of protein function by enrichment and depletion of variants.
Enrich: software for analysis of protein function by enrichment and depletion of variants.
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DOI：
10.1093/bioinformatics/btr577
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发表时间：
2011-12-15
期刊：
影响因子：
--
通讯作者：
Fields S
中科院分区：
文献类型：
--
作者：
Fowler DM;Araya CL;Gerard W;Fields S
摘要：测量蛋白质突变的后果对于理解它们的功能至关重要。这些测量在蛋白质工程、药物开发、蛋白质设计和基因组序列分析等应用中是必不可少的。最近，高通量测序已与蛋白质活性分析相结合，使并行分析大量突变成为可能。我们提出了一种分析这种深度突变扫描数据的工具--ENRIME。Enrich在高通量测序数据集中识别蛋白质的所有独特变体(突变体)，并可以使用重叠的配对末端读取来纠正测序错误。丰富使用每个变异在选择前后的频率来计算富集率，该富集率被用来估计适应度。Enrich提供了一个交互界面来指导用户。它为下游分析生成用户可访问的输出，以及突变对功能影响的几个可视化，从而使用户能够快速量化和理解序列-功能关系。可用性和实现：Enrich是用PYTHON实现的，并且可以在http://depts.washington.edu/sfields/software/enrich/.上获得免费BSD许可丰富包括详细的文档和一个小的示例数据集。联系方式：dfowler@uw.edu；field@uw.edu补充信息：补充数据可在BioInformation Online上获得。
Summary: Measuring the consequences of mutation in proteins is critical to understanding their function. These measurements are essential in such applications as protein engineering, drug development, protein design and genome sequence analysis. Recently, high-throughput sequencing has been coupled to assays of protein activity, enabling the analysis of large numbers of mutations in parallel. We present Enrich, a tool for analyzing such deep mutational scanning data. Enrich identifies all unique variants (mutants) of a protein in high-throughput sequencing datasets and can correct for sequencing errors using overlapping paired-end reads. Enrich uses the frequency of each variant before and after selection to calculate an enrichment ratio, which is used to estimate fitness. Enrich provides an interactive interface to guide users. It generates user-accessible output for downstream analyses as well as several visualizations of the effects of mutation on function, thereby allowing the user to rapidly quantify and comprehend sequence–function relationships. Availability and Implementation: Enrich is implemented in Python and is available under a FreeBSD license at http://depts.washington.edu/sfields/software/enrich/. Enrich includes detailed documentation as well as a small example dataset. Contact: dfowler@uw.edu; fields@uw.edu Supplementary Information: Supplementary data is available at Bioinformatics online.
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