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RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
Wang, Jinpeng1,2,3,5; Li, Li1,4,5; Qi, Haigang1,3,5; Dua, Xuedi1,3,5; Zhang, Guofan1,3,5
2016-05-01
Source PublicationELECTRONIC JOURNAL OF BIOTECHNOLOGY
Volume21Pages:36-42
SubtypeArticle
AbstractBackground: Reduced-representation sequencing technology is widely used in genotyping for its economical and efficient features. A popular way to construct the reduced-representation sequencing libraries is to digest the genomic DNA with restriction enzymes. A key factor of this method is to determine the restriction enzyme(s). But there are few computer programs which can evaluate the usability of restriction enzymes in reduced-representation sequencing. SimRAD is an R package which can simulate the digestion of DNA sequence by restriction enzymes and return enzyme loci number as well as fragment number. But for linkage mapping analysis, enzyme loci distribution is also an important factor to evaluate the enzyme. For phylogenetic studies, comparison of the enzyme performance across multiple genomes is important. It is strongly needed to develop a simulation tool to implement these functions.
KeywordGenotyping Reduced-representation Libraries Reduced-representation Sequencing
DOI10.1016/j.ejbt.2016.02.003
Indexed BySCI
Language英语
WOS IDWOS:000376595900005
Citation statistics
Document Type期刊论文
Version出版稿
Identifierhttp://ir.qdio.ac.cn/handle/337002/131085
Collection海洋生物技术研发中心
Affiliation1.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100039, Peoples R China
3.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266071, Peoples R China
4.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Fisheries & Aquaculture, Qingdao 266071, Peoples R China
5.Natl & Local Joint Engn Lab Ecol Mariculture, Qingdao 266071, Peoples R China
First Author AffilicationKey Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Wang, Jinpeng,Li, Li,Qi, Haigang,et al. RestrictionDigest: A powerful Perl module for simulating genomic restriction digests[J]. ELECTRONIC JOURNAL OF BIOTECHNOLOGY,2016,21:36-42.
APA Wang, Jinpeng,Li, Li,Qi, Haigang,Dua, Xuedi,&Zhang, Guofan.(2016).RestrictionDigest: A powerful Perl module for simulating genomic restriction digests.ELECTRONIC JOURNAL OF BIOTECHNOLOGY,21,36-42.
MLA Wang, Jinpeng,et al."RestrictionDigest: A powerful Perl module for simulating genomic restriction digests".ELECTRONIC JOURNAL OF BIOTECHNOLOGY 21(2016):36-42.
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