A fast and flexible approach to oligonucleotide probe design for genomes and gene families

doi:10.1093/bioinformatics/btm114

	A fast and flexible approach to oligonucleotide probe design for genomes and gene families
	Feng, Shengzhong ; Tillier, Elisabeth R. M.
	2007-05-15
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	23 期号:10 页码:1195-1202
摘要	Motivation: With hundreds of completely sequenced microbial genomes available, and advancements in DNA microarray technology, the detection of genes in microbial communities consisting of hundreds of thousands of sequences may be possible. The existing strategies developed for DNA probe design, geared toward identifying specific sequences, are not suitable due to the lack of coverage, flexibility and efficiency necessary for applications in metagenomics. Methods: ProDesign is a tool developed for the selection of oligonucleotide probes to detect members of gene families present in environmental samples. Gene family-specific probe sequences are generated based on specific and shared words, which are found with the spaced seed hashing algorithm. To detect more sequences, those sharing some common words are re-clustered into new families, then probes specific for the new families are generated. Results: The program is very flexible in that it can be used for designing probes for detecting many genes families simultaneously and specifically in one or more genomes. Neither the length nor the melting temperature of the probes needs to be predefined. We have found that ProDesign provides more flexibility, coverage and speed than other software programs used in the selection of probes for genomic and gene family arrays.
DOI	10.1093/bioinformatics/btm114
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:000247348300003
出版者	OXFORD UNIV PRESS
引用统计	被引频次：27[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/2XEOYT63/10886
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Tillier, Elisabeth R. M.
作者单位	1.Univ Hlth Network, Ontario Canc Inst, Toronto, ON, Canada 2.Chinese Acad Sci, Inst Comp Technol, Beijing 100864, Peoples R China 3.Univ Toronto, Dept Med Biophys, Toronto, ON, Canada
推荐引用方式 GB/T 7714	Feng, Shengzhong,Tillier, Elisabeth R. M.. A fast and flexible approach to oligonucleotide probe design for genomes and gene families[J]. BIOINFORMATICS,2007,23(10):1195-1202.
APA	Feng, Shengzhong,&Tillier, Elisabeth R. M..(2007).A fast and flexible approach to oligonucleotide probe design for genomes and gene families.BIOINFORMATICS,23(10),1195-1202.
MLA	Feng, Shengzhong,et al."A fast and flexible approach to oligonucleotide probe design for genomes and gene families".BIOINFORMATICS 23.10(2007):1195-1202.