OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes.
OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes.
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DOI：
10.1073/pnas.1714530115
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发表时间：
2018-03-06
影响因子：
11.1
通讯作者：
Yin P
中科院分区：
文献类型：
--
作者：
Beliveau BJ;Kishi JY;Nir G;Sasaki HM;Saka SK;Nguyen SC;Wu CT;Yin P
FISH使研究人员能够可视化单个细胞中RNA和DNA分子的亚细胞分布。采用由合成DNA寡核苷酸（oligos）组成的探针的FISH方法的最新发展允许研究人员严格控制探针设计的方面，例如结合能和基因组特异性。虽然寡FISH探针是许多最近开发的大规模多路复用和超分辨率成像方法的核心，但不存在专用的计算实用程序来促进在全基因组范围内设计此类探针。在这里，我们介绍了一个精简的流水线，用于快速，基因组规模的寡核苷酸FISH探针的设计，并通过使用常规和超分辨率成像验证我们的方法。我们的方法提供了一个框架，设计寡核苷酸为基础的杂交实验。基于寡核苷酸（oligo）的FISH已经成为研究染色体组织和基因表达的重要工具，并且已经被高度复杂的oligo池的商业可用性所授权。然而，一个专门的生物信息学设计实用程序尚未创建专门用于在全基因组范围内识别最佳寡核苷酸FISH探针序列的目的。在这里，我们介绍了OligoMiner，这是一种快速而强大的计算管道，用于寡核苷酸FISH探针的基因组规模设计，为科学家提供对每个探针参数的精确控制。我们的简化方法使用标准的生物信息学文件格式，允许用户根据需要将新的和现有的实用程序无缝集成到管道中，并引入了一种用于评估每个探针分子特异性的方法，该方法将模拟杂交能量学与使用监督机器学习快速生成的序列比对连接起来。我们通过在许多模式生物基因组中进行基因组规模的探针发现来证明我们方法的可扩展性，并展示了所得探针的性能，这些探针具有染色体和RNA靶标的衍射限制和单分子超分辨率成像。我们预计，这条管道将使FISH探针设计过程更容易，并将更广泛地促进杂交探针池的设计，用于各种应用。
FISH enables researchers to visualize the subcellular distribution of RNA and DNA molecules in individual cells. The recent development of FISH methods employing probes composed of synthetic DNA oligonucleotides (oligos) allows researchers to tightly control aspects of probe design such as binding energy and genomic specificity. Although oligo FISH probes are central to many recently developed massively multiplexed and superresolution imaging methods, no dedicated computational utility exists to facilitate the design of such probes on the genome-wide scale. Here, we introduce a streamlined pipeline for the rapid, genome-scale design of oligo FISH probes and validate our approach by using conventional and superresolution imaging. Our method provides a framework with which to design oligo-based hybridization experiments. Oligonucleotide (oligo)-based FISH has emerged as an important tool for the study of chromosome organization and gene expression and has been empowered by the commercial availability of highly complex pools of oligos. However, a dedicated bioinformatic design utility has yet to be created specifically for the purpose of identifying optimal oligo FISH probe sequences on the genome-wide scale. Here, we introduce OligoMiner, a rapid and robust computational pipeline for the genome-scale design of oligo FISH probes that affords the scientist exact control over the parameters of each probe. Our streamlined method uses standard bioinformatic file formats, allowing users to seamlessly integrate new and existing utilities into the pipeline as desired, and introduces a method for evaluating the specificity of each probe molecule that connects simulated hybridization energetics to rapidly generated sequence alignments using supervised machine learning. We demonstrate the scalability of our approach by performing genome-scale probe discovery in numerous model organism genomes and showcase the performance of the resulting probes with diffraction-limited and single-molecule superresolution imaging of chromosomal and RNA targets. We anticipate that this pipeline will make the FISH probe design process much more accessible and will more broadly facilitate the design of pools of hybridization probes for a variety of applications.
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影响因子：
38.3
作者：
通讯作者：
--
影响因子：
12.3
作者：
Carpenter AE;Jones TR;Lamprecht MR;Clarke C;Kang IH;Friman O;Guertin DA;Chang JH;Lindquist RA;Moffat J;Golland P;Sabatini DM
通讯作者：
Sabatini DM
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：
Bienko, Magda;Crosetto, Nicola;Teytelman, Leonid;Klemm, Sandy;Itzkovitz, Shalev;van Oudenaarden, Alexander
通讯作者：
van Oudenaarden, Alexander
影响因子：
56.9
作者：
Femino, A;Fay, FS;Singer, RH
通讯作者：
Singer, RH