Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping
文献类型：期刊论文
| 作者 | Ren, Xiaoliang4; Shao, Yanwen2; Zhang, Yiwen2; Ni, Ying1,3; Bi, Yu2; Li, Runsheng2,5 |
| 刊名 | BIOINFORMATICS
 |
| 出版日期 | 2023-04-03 |
| 卷号 | 39期号:4页码:2 |
| ISSN号 | 1367-4803 |
| DOI | 10.1093/bioinformatics/btad188 |
| 通讯作者 | Li, Runsheng(runsheng.li@cityu.edu.hk) |
| 英文摘要 | Motivation: Primer design is a routine practice for modern molecular biology labs. Bioinformatics tools like primer3 and primer-blast have standardized the primer design for a specific region. However, large-scale primer design, especially for genome-wide screening, is still a labor-intensive job for most wet-lab researchers using these pipelines.Results: Here, we present the primerdiffer pipeline, which can be used to batch design primers that differentiate haplotypes on a large scale with precise false priming checking. This command-line interface (CLI) pipeline includes greedy primer search, local and global in silico PCR-based false priming checking, and automated best primer selection. The local CLI application provides flexibility to design primers with the user's own genome sequences and specific parameters. Some species-specific primers designed to genotype the hybrid introgression strains from Caenorhabditis briggsae and Caenorhabditis nigoni have been validated using single-worm PCR. This pipeline provides the first CLI-based large-scale primer design tool to differentiate haplotypes in any targeted region. |
| 资助项目 | Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)[SMSEGL20SC02] ; Hong Kong Research Grant Council[9048204] ; Hong Kong Health and Medical Research Fund[9211280] ; City University of Hong Kong[9610497] |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics |
| 语种 | 英语 |
| 出版者 | OXFORD UNIV PRESS |
| WOS记录号 | WOS:000976245900006 |
| 源URL | [http://ir.qdio.ac.cn/handle/337002/182978]  |
| 专题 | 海洋研究所_海洋生物分类与系统演化实验室 |
| 通讯作者 | Li, Runsheng |
| 作者单位 | 1.City Univ Hong Kong, Tung Biomed Sci Ctr, Hong Kong, Peoples R China 2.City Univ Hong Kong, Jockey Club Coll Vet Med & Life Sci, Dept Infect Dis & Publ Hlth, Hong Kong, Peoples R China 3.City Univ Hong Kong, Dept Biomed Sci, Hong Kong, Peoples R China 4.Chinese Acad Sci, Inst Oceanol, Lab Marine Organism Taxon & Phylogeny, Qingdao Key Lab Marine Biodivers & Conservat, Qingdao 266071, Peoples R China 5.Southern Marine Sci & Engn Guangdong Lab Guangzhou, Guangzhou, Peoples R China |
| 推荐引用方式 GB/T 7714 | Ren, Xiaoliang,Shao, Yanwen,Zhang, Yiwen,et al. Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping[J]. BIOINFORMATICS,2023,39(4):2. |
| APA | Ren, Xiaoliang,Shao, Yanwen,Zhang, Yiwen,Ni, Ying,Bi, Yu,&Li, Runsheng.(2023).Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping.BIOINFORMATICS,39(4),2. |
| MLA | Ren, Xiaoliang,et al."Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping".BIOINFORMATICS 39.4(2023):2. |
入库方式： OAI收割
来源：海洋研究所
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