NCBIminer: sequences harvest from Genbank

doi:10.1111/ecog.01055

CORC > 北京大学 > 城市与环境学院

	NCBIminer: sequences harvest from Genbank
	Xu, Xiaoting ; Dimitrov, Dimitar ; Rahbek, Carsten ; Wang, Zhiheng
刊名	ECOGRAPHY
	2015
DOI	10.1111/ecog.01055
英文摘要	NCBIminer is freely available, cross-platform and user-friendly software for mining nucleotide sequence data from GenBank. It has several features that enable users to accurately and efficiently download sequences with specific attributes from the GenBank database: 1) it uses a novel search strategy, and can download sequences for distantly related taxonomic groups with high accuracy; 2) it deals with genes, CDS, rRNA, and other GenBank-defined feature types; 3) it can filter sequences by length and similarities with the reference sequence using user-defined parameters; 4) it can download information on DNA sample collections, e.g. voucher specimen, country, latitude and longitude, and collector; 5) it takes advantage of parallelization for a high efficiency workflow. We demonstrate the use and performance of NCBIminer by downloading sequences for the plant family Campanulaceaes. Compared to other methods, NCBIminer harvests more and longer sequences, and is less sensitive to query sequences.; Chinese Scholarship Council; Marie Curie Actions [PIEF-GA-2010-275666]; Danish National Research Foundation; National Natural Science Foundation of China [31470564, 31400467, 31321061]; 111 Project [B14001]; SCI(E); ARTICLE; zhiheng.wang@pku.edu.cn; 4,SI; 426-430; 38
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/420623]
专题	城市与环境学院
推荐引用方式 GB/T 7714	Xu, Xiaoting,Dimitrov, Dimitar,Rahbek, Carsten,et al. NCBIminer: sequences harvest from Genbank[J]. ECOGRAPHY,2015.
APA	Xu, Xiaoting,Dimitrov, Dimitar,Rahbek, Carsten,&Wang, Zhiheng.(2015).NCBIminer: sequences harvest from Genbank.ECOGRAPHY.
MLA	Xu, Xiaoting,et al."NCBIminer: sequences harvest from Genbank".ECOGRAPHY (2015).