GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and VIewing

doi:10.3389/fpls.2016.01350

	GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and VIewing
	Wang, Xuewen; Wang, Le
	2016-09-13
发表期刊	FRONTIERS IN PLANT SCIENCE
卷号	7
摘要	imple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar.
关键词	Ssr Software Marker Polymorphism And Transferability Statistical Graph Gbrowser Display Grass Genome Ssr Pattern
DOI	10.3389/fpls.2016.01350
收录类别	SCI
语种	英语
WOS记录号	WOS:000382913700001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/28601
专题	中国西南野生生物种质资源库
推荐引用方式 GB/T 7714	Wang, Xuewen,Wang, Le. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and VIewing[J]. FRONTIERS IN PLANT SCIENCE,2016,7.
APA	Wang, Xuewen,&Wang, Le.(2016).GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and VIewing.FRONTIERS IN PLANT SCIENCE,7.
MLA	Wang, Xuewen,et al."GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and VIewing".FRONTIERS IN PLANT SCIENCE 7(2016).

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