热门
GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and VIewing
文献类型：期刊论文
| 作者 | Wang, Xuewen; Wang, Le |
| 刊名 | FRONTIERS IN PLANT SCIENCE
 |
| 出版日期 | 2016-09-13 |
| 卷号 | 7 |
| 关键词 | SSR software marker polymorphism and transferability statistical graph Gbrowser display grass genome SSR pattern |
| 英文摘要 | 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. |
| 类目[WOS] | Plant Sciences |
| 研究领域[WOS] | Plant Sciences |
| 关键词[WOS] | TANDEM REPEATS ; MICROSATELLITE MARKERS ; WIDE ; SEQUENCES ; DATABASE ; SETARIA ; MAIZE |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000382913700001 |
| 源URL | [http://ir.kib.ac.cn/handle/151853/28601]  |
| 专题 | 昆明植物研究所_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). |
入库方式： OAI收割
来源：昆明植物研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。