CMD: a Cotton Microsatellite Database resource for Gossypium genomics.
CMD: a Cotton Microsatellite Database resource for Gossypium genomics.
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DOI：
10.1186/1471-2164-7-132
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发表时间：
2006-05-31
期刊：
影响因子：
4.4
通讯作者：
Main D
中科院分区：
文献类型：
--
作者：
Blenda A;Scheffler J;Scheffler B;Palmer M;Lacape JM;Yu JZ;Jesudurai C;Jung S;Muthukumar S;Yellambalase P;Ficklin S;Staton M;Eshelman R;Ulloa M;Saha S;Burr B;Liu S;Zhang T;Fang D;Pepper A;Kumpatla S;Jacobs J;Tomkins J;Cantrell R;Main D
棉花微卫星数据库（CMD）是一个精心策划的综合性网络关系数据库，提供对公开的棉花微卫星的集中访问，这是棉花育种基础和应用研究的宝贵资源。目前，CMD包含9个主要棉花微卫星项目的出版物、序列、引物、作图和同源性数据，共代表5，484个微卫星。此外，CMD还展示了三个微卫星项目的数据，这些项目已经针对一组核心种质进行了筛选。标准化的样本组由12种不同的基因型组成，包括遗传标准、作图亲本、BAC供体、亚基因组代表、独特的育种系、外来渐渗来源和具有显著种植面积的当代高地棉花。CMD提供一套在线微卫星数据挖掘工具。这些服务器包括鉴定微卫星、引物、开放阅读框架和上传序列的GC含量的SSR服务器;提供针对现有棉花SSR序列和引物的序列相似性搜索的BLAST和FASTA服务器;在挖掘SSR之前将EST序列组装成较长转录本的CAP 3服务器;以及用于比较棉花SSR图谱的查看器CMap。将公开可用的棉花SSR标记收集在一个集中的、易于访问的和管理的网络数据库中，可以更有效地利用微卫星资源，并将有助于加快棉花分子育种和遗传作图的基础和应用研究。
The Cotton Microsatellite Database (CMD) is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps. The collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp.