PMDBase: a database for studying microsatellite DNA and marker development in plants.
PMDBase: a database for studying microsatellite DNA and marker development in plants.
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DOI：
10.1093/nar/gkw906
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发表时间：
2017-01-04
影响因子：
14.9
通讯作者：
Zhang X
中科院分区：
文献类型：
--
作者：
Yu J;Dossa K;Wang L;Zhang Y;Wei X;Liao B;Zhang X
微卫星DNA（或SSR）是基因组的重要组成部分，参与许多重要的生物学功能。SSR标记在遗传多样性、基因/QTL的连锁/关联定位、标记辅助选择、品种鉴定和进化分析等方面有着广泛的应用。然而，一个全面的数据库或网络服务，研究微卫星DNA和标记的发展在植物中是缺乏的。在这里，我们开发了一个数据库，PMDBase，它集成了大量的微卫星DNA从基因组测序的植物物种，并包括一个网络服务的微卫星DNA鉴定。在PMDBase中共检测到26 230 099个微卫星DNA，分布于110种植物。每个微卫星DNA最多提供三对引物。对于81个物种，微卫星DNA（基因或非基因）的基因组特征与公共数据库中相应的基因或转录本一起提供。可通过浏览和搜索模块，利用用户友好的网络界面和定制软件，探索微卫星DNA。此外，我们还开发了MISAweb和嵌入式Primer 3 web，帮助用户在线识别微卫星DNA，并在自己的基因组序列中设计相应的引物。可以方便地下载所有微卫星DNA数据集。PMDBase将定期更新新的可用基因组数据，并可通过地址http://www.sesame-bioinfo.org/PMDBase免费访问。
Microsatellite DNAs (or SSRs) are important genomic components involved in many important biological functions. SSRs have been extensively exploited as molecular markers for diverse applications including genetic diversity, linkage/association mapping of gene/QTL, marker-assisted selection, variety identification and evolution analysis. However, a comprehensive database or web service for studying microsatellite DNAs and marker development in plants is lacking. Here, we developed a database, PMDBase, which integrates large amounts of microsatellite DNAs from genome sequenced plant species and includes a web service for microsatellite DNAs identification. In PMDBase, 26 230 099 microsatellite DNAs were identified spanning 110 plant species. Up to three pairs of primers were supplied for every microsatellite DNA. For 81 species, genomic features of the microsatellite DNAs (genic or non-genic) were supplied with the corresponding genes or transcripts from public databases. Microsatellite DNAs can be explored through browsing and searching modules with a user-friendly web interface and customized software. Furthermore, we developed MISAweb and embedded Primer3web to help users to identify microsatellite DNAs and design corresponding primers in their own genomic sequences online. All datasets of microsatellite DNAs can be downloaded conveniently. PMDBase will be updated regularly with new available genome data and can be accessed freely via the address http://www.sesame-bioinfo.org/PMDBase.
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影响因子：
2.4
作者：
Shirasawa K;Isobe S;Tabata S;Hirakawa H
通讯作者：
Hirakawa H
影响因子：
14.9
作者：
Federhen S
通讯作者：
Federhen S
栽培辣椒和野生辣椒的全基因组测序为辣椒驯化和专业化提供了见解
DOI：
10.1073/pnas.1400975111
发表时间：
2014-04-08
影响因子：
11.1
作者：
Qin, Cheng;Yu, Changshui;Zhang, Zhiming
通讯作者：
Zhang, Zhiming
影响因子：
14.9
作者：
Huala, E;Dickerman, AW;Rhee, SY
通讯作者：
Rhee, SY
影响因子：
5.3
作者：
Iquebal MA; S;Arora V;Verma N;Rai A;Kumar D
通讯作者：
Kumar D