Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping

doi:10.1093/bioinformatics/btad188

	Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping
	Ren, Xiaoliang 1; Shao, Yanwen 2; Zhang, Yiwen 2; Ni, Ying 3,4; Bi, Yu 2; Li, Runsheng 2,5
	2023-04-03
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	39 期号:4 页码:2
通讯作者	Li, Runsheng(runsheng.li@cityu.edu.hk)
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.
DOI	10.1093/bioinformatics/btad188
收录类别	SCI
语种	英语
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
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000976245900006
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/182979
专题	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.Chinese Acad Sci, Inst Oceanol, Lab Marine Organism Taxon & Phylogeny, Qingdao Key Lab Marine Biodivers & Conservat, Qingdao 266071, 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.City Univ Hong Kong, Tung Biomed Sci Ctr, Hong Kong, Peoples R China 5.Southern Marine Sci & Engn Guangdong Lab Guangzhou, Guangzhou, Peoples R China
第一作者单位	中国科学院海洋研究所
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.