IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics

doi:10.1093/bioinformatics/btl410

	IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics
	Li, Dequan ; Gao, Wen ; Ling, Charles X.; Wang, Xiaobiao ; Sun, Ruixiang ; He, Simin
	2006-10-15
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	22 期号:20 页码:2572-2573
摘要	A software package, IndexToolkit, aimed at overcoming the disadvantage of FASTA-format databases for frequent searching, is developed to utilize an indexing strategy to substantially accelerate sequence queries. IndexToolkit includes user-friendly tools and an Application Programming Interface (API) to facilitate indexing, storage and retrieval of protein sequence databases. As open source, it provides a sequence-retrieval developing framework, which is easily extensible for high-speed-request proteomic applications, such as database searching or modification discovering. We applied IndexToolkit to database searching engine pFind to demonstrate its effect. Experimental studies show that IndexToolkit is able to support significantly faster searches of protein database.
DOI	10.1093/bioinformatics/btl410
收录类别	SCI
语种	英语
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:000241271300023
出版者	OXFORD UNIV PRESS
引用统计	被引频次：4[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/10382
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Li, Dequan
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Beijing 100080, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China 3.Univ Western Ontario, Dept Comp Sci, London, ON N6A 3K7, Canada
推荐引用方式 GB/T 7714	Li, Dequan,Gao, Wen,Ling, Charles X.,et al. IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics[J]. BIOINFORMATICS,2006,22(20):2572-2573.
APA	Li, Dequan,Gao, Wen,Ling, Charles X.,Wang, Xiaobiao,Sun, Ruixiang,&He, Simin.(2006).IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics.BIOINFORMATICS,22(20),2572-2573.
MLA	Li, Dequan,et al."IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics".BIOINFORMATICS 22.20(2006):2572-2573.