All output discussed in the previous section was loaded into a MySQL database with user-searchable CGI scripts. There are four main ways to search within the PlantTribes Database (Figure 2): (i) using a gene ID or annotation term for any of the Arabidopsis, rice, Populus, Medicago or papaya gene models; (ii) using a CDD domain accession ID, name or description; (iii) running a BLAST search on a single sequence or file of user-supplied sequences or (iv) querying the database of tribe characteristics. For example, all tribes with a minimum and/or maximum tribe size for each species or a threshold cumulative gene number can be retrieved with a simple query. HTML formatted search results include hyperlinks to sequence information, domain content and the tribes represented by each hit. All search results have links to the main page for each tribe within the database. Each tribe page includes the following information: unified annotation, stringency, SuperTribe identifier, the number of sequences from each species, all CDD entries for each of the genes in the tribe, a list of the genes in the tribe as well as each gene's tribe identifier at low, medium and high stringency. Tribe stability can be readily examined through comparison of tribe membership at the different stringencies. Tools are also provided to view sequences from other species that have been sorted into each tribe and to view and/or download the sequences, alignments (constructed at both protein and DNA level) and phylogenetic trees in all major formats for each tribe.
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