All the available data for each species is easily found through their Overview page. From the CottonGen homepage, these are accessed either by selecting them in the Species menu in the toolbar (Fig. 3A) or from the Major Species Quick Start section (Fig. 3B).
Figure 3. Accessing the Species Overview pages from the homepage.
On each Species Overview page, there are two main sections. The left side toolbar is static and has a Data section and a Tools section (Fig. 4A). The links in these sections either change the information to the right of the toolbar (Fig. 4B), or open another tab with the linked information. Species Overview pages default to the Overview section which contains basic information and a summary of related CottonGen data.
Figure 4. CottonGen Species Overview page.
Many of the left toolbar links will dynamically change the displayed content (Fig. 5). The Genome link displays a list of assemblies for that species, which in turn go to Genome Overview pages with relevant information and analytical funtions. Similarly, Germplasm will display a list of germplasms for that species in CottonGen that can be used to view Germplasm Overview pages and data. Selecting Transcripts brings up a table with summary information for the RefTrans and Unigene assemblies with links to further information.
Figure 5. Dynamic data.
The rest of the left toolbar links open new tabs. For example, the Genetic Maps link opens a new tab that has a table of all the genetic maps in CottonGen (Fig. 6), with links to detailed information. Under Tools, CMap allows for viewing and comparing genetic maps available in CottonGen, while MapViewer visualizes marker locations by genetic map and linkage group. Please refer to the appropriate tutorials for more information on using these datasets and tools.
Figure 6. Genetic Map page and example of detailed information available under hyperlink.