Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for saturation genome editing and other deep mutational scanning experiments.
Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for saturation genome editing and other deep mutational scanning experiments.
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DOI：
10.1093/bioinformatics/btab776
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发表时间：
2022-01-27
期刊：
影响因子：
--
通讯作者：
Waters AJ
中科院分区：
文献类型：
--
作者：
Barbon L;Offord V;Radford EJ;Butler AP;Gerety SS;Adams DJ;Tan HK;Waters AJ
基于CRISPR/Cas9的技术允许以单核苷酸分辨率对遗传变异进行功能分析，同时保持基因组背景。这种方法被称为饱和基因组编辑（SGE），是一种深度突变扫描，系统地改变目标区域中的每个位置以探索其功能。SGE实验需要设计和合成引入基因组的寡核苷酸变体文库。该技术适用于多种领域，如疾病变体鉴定、药物开发、结构-功能研究、合成生物学、进化遗传学和宿主-病原体相互作用。在这里，我们提出了变体库注释工具（VaLiAnT），它可以用于从用户定义的基因组坐标和标准输入文件生成变体库。该软件可以适应用户指定的物种，参考序列和转录本注释。用户提供基因组范围的坐标以检索相应的寡核苷酸参考序列。然后，该序列内的用户指定的范围经受系统的、核苷酸和/或氨基酸饱和的增变子功能。VaLiAnT提供了一种新的方法来检索，突变和注释基因组序列，用于寡核苷酸文库的生成。可以采用用于SGE文库生成的特定特征。此外，VaLiAnT是可配置的，允许cDNA和引物编辑饱和文库生成，以及其他不同的应用。VaLiAnT是一个用Python编写的命令行工具。除了详细的用户手册（https：//github.com/cancerit/VaLiAnT/wiki）外，还提供源代码、测试数据、示例输入和输出文件以及可执行文件（https：//github.com/cancerit/VaLiAnT/wiki）。VaLiAnT在AGPLv 3下获得许可。 补充数据可在Bioinformatics在线获得。
CRISPR/Cas9-based technology allows for the functional analysis of genetic variants at single nucleotide resolution whilst maintaining genomic context. This approach, known as saturation genome editing (SGE), a form of deep mutational scanning, systematically alters each position in a target region to explore its function. SGE experiments require the design and synthesis of oligonucleotide variant libraries which are introduced into the genome. This technology is applicable to diverse fields such as disease variant identification, drug development, structure–function studies, synthetic biology, evolutionary genetics and host–pathogen interactions. Here, we present the Variant Library Annotation Tool (VaLiAnT) which can be used to generate variant libraries from user-defined genomic coordinates and standard input files. The software can accommodate user-specified species, reference sequences and transcript annotations. Coordinates for a genomic range are provided by the user to retrieve a corresponding oligonucleotide reference sequence. A user-specified range within this sequence is then subject to systematic, nucleotide and/or amino acid saturating mutator functions. VaLiAnT provides a novel way to retrieve, mutate and annotate genomic sequences for oligonucleotide library generation. Specific features for SGE library generation can be employed. In addition, VaLiAnT is configurable, allowing for cDNA and prime editing saturation library generation, with other diverse applications possible. VaLiAnT is a command line tool written in Python. Source code, testing data, example input and output files and executables are available (https://github.com/cancerit/VaLiAnT) in addition to a detailed user manual (https://github.com/cancerit/VaLiAnT/wiki). VaLiAnT is licensed under AGPLv3. Supplementary data are available at Bioinformatics online.
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影响因子：
64.8
作者：
Findlay GM;Daza RM;Martin B;Zhang MD;Leith AP;Gasperini M;Janizek JD;Huang X;Starita LM;Shendure J
通讯作者：
Shendure J
DOI：
10.1093/bioinformatics/btv308
发表时间：
2015-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Hodgkins A;Farne A;Perera S;Grego T;Parry-Smith DJ;Skarnes WC;Iyer V
通讯作者：
Iyer V
影响因子：
7.7
作者：
Jones EM;Lubock NB;Venkatakrishnan AJ;Wang J;Tseng AM;Paggi JM;Latorraca NR;Cancilla D;Satyadi M;Davis JE;Babu MM;Dror RO;Kosuri S
通讯作者：
Kosuri S
影响因子：
7
作者：
Kan Y;Ruis B;Takasugi T;Hendrickson EA
通讯作者：
Hendrickson EA
影响因子：
64.8
作者：
Karczewski, Konrad J;Francioli, Laurent C;MacArthur, Daniel G
通讯作者：
MacArthur, Daniel G