PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments.
PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments.
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DOI：
10.1038/s41592-021-01187-3
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发表时间：
2021-08
期刊：
影响因子：
48
通讯作者：
Beliveau BJ
中科院分区：
文献类型：
--
作者：
Hershberg EA;Camplisson CK;Close JL;Attar S;Chern R;Liu Y;Akilesh S;Nicovich PR;Beliveau BJ
荧光原位杂交(FISH)使研究人员能够可视化固定样本中核酸的空间位置和数量。最近，基于寡核苷酸的FISH方法取得了长足的进展，使研究人员能够以超分辨率研究基因组的三维组织，并可视化单个细胞中数千个基因的基因表达的空间模式。然而，几乎没有现有的计算工具来支持利用寡头鱼类探针进行这些实验所需的生物信息学工作流程。在这里，我们介绍了Paint Server和同源优化管道(Paintshop)，这是一个用于设计寡头鱼实验的交互平台。Paintshop使研究人员能够有效地为他们的实验目标识别探针，加入额外的必要序列，如引物对，并容易地生成文档库设计的文件。Paintshop使为寡头鱼群落设计复杂的探测组的过程民主化和标准化。Paint服务器和同源优化管道(Paintshop)是一个用于设计寡鱼实验的交互平台，它使为寡鱼群落设计复杂探针组的过程民主化和标准化。
Fluorescence in situ hybridization (FISH) allows researchers to visualize the spatial position and quantity of nucleic acids in fixed samples. Recently, considerable progress has been made in developing oligonucleotide (oligo)-based FISH methods that have enabled researchers to study the three-dimensional organization of the genome at super-resolution and visualize the spatial patterns of gene expression for thousands of genes in individual cells. However, there are few existing computational tools to support the bioinformatics workflows necessary to carry out these experiments utilizing oligo FISH probes. Here, we introduce Paint Server and Homology Optimization Pipeline (PaintSHOP), an interactive platform for the design of oligo FISH experiments. PaintSHOP enables researchers to identify probes for their experimental targets efficiently, to incorporate additional necessary sequences such as primer pairs, and to easily generate files documenting library design. PaintSHOP democratizes and standardizes the process of designing complex probe sets for the oligo FISH community. Paint Server and Homology Optimization Pipeline (PaintSHOP), an interactive platform for the design of oligo FISH experiments, democratizes and standardizes the process of designing complex probe sets for the oligo FISH community.
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Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
48
作者：
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通讯作者：
van Oudenaarden, Alexander
影响因子：
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影响因子：
56.9
作者：
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Singer, RH
影响因子：
3
作者：
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