logo

֍ Version 1.0
֍ Quick GO
֍ Search PMDBase


WWW SITE

Pipeline of this project

Instruction: In this project, we designed three steps to curate microsatellite DNAs or SSRs in 110 plant species, which have complete genome sequences. For the first step, we download genomic sequences of 110 plant species from public species-specific genomic database. In order to identify microsatellite DNAs or SSRs, we employed perl scripts from MISA and combined our in-house Perl and Python scripts to develop the workflow for identifying microsatellite DNAs or SSRs. In the second step, we curated the datasets of microsatellite DNAs or SSRs to construct user-friendly plant microsatellite DNAs database. And then, we used the identified microsatellite DNAs to develop the SSR markers in different plant species. At last step, we used the datasets of microsatellite DNAs to detect the difference among different plant species, which will supply some evidences of plant genome evolution.

pipeline

Overview of this database

Instruction: In PMDBase, we designed five functional units to illustrate plant microsatellite DNAs or SSRs to scientists in community. These five functional units includes home, browse, tools, document, help and community. Out of these functional units, 'Browse' and 'Tools' are two important functional units. From the 'Browse' functional unit, users can obtain the whole information of plant microsatellite DNAs or SSRs in this database. In 'Tools' functional unit, we embeded several customized open resource software, such as BLAST and GBrowse, which can be used to display the location of microsatellite DNAs. Moreover, we developed user-friendly MISAweb, which can help users to identify microsatellite DNAs in genomic sequences online. The MISAweb will bring convinent for scientists, which were not familiar with perl language programming. From MISAweb, they can identify microsatellite DNAs in their interested genomic sequences. In 'Tools', we also embedded Primer3web in our database, which will help users to design primers of their microsatellite DNAs quickly.

pipeline

2016@All copyrights are reserved by Department of Sesame Germplasm Resources at Oil Crops Research Institute.
For suggestions, please contact web administrator
IE 8.0 or more higher & 1366×1024 resolution suggested