A ZmGDB context page focused on a Zea mays BAC assembly (accession Z474J15; GenBank id 48374974). A site header contains site navigation and search controls (items 1 and 2). Links to integrated webservices (item 3) and context navigation controls (item 4) are available. The feature control panel (item 5) and context graphic shows yrGATE community annotations (item 7), GenBank gene features (item 8), PlantGDB GSS assemblies (item 9), rice predicted protein alignments (item 10), cDNA alignments (item 11), EST alignments (item 12), PlantGDB Unique Transcript alignments (item 13), and MaizeArray microarray probe alignments (item 14) in the genomic region spanning bases 45,001 to 55,000 (item 6) of the assembled sequence. Exon features are displayed as filled rectangles connected by intronic features represented by similarly colored lines. Predicted start and stop codons of open reading frames are represented by green and red triangles, respectively. Arrowheads represent genomic strand orientation when this can be determined. Noncognate features are represented by alternative feature colors (pink for EST and grey for cDNA features). BAC, bacterial artificial chromosome; EST, expressed sequence tag; GSS, genome survey sequence.

Search results at AtGDB using the query +"fatty acid desaturase" -"omega-3". The '+' and '-' operators represent inclusion and exclusion, respectively, following the convention of MySQL boolean text searches [39].

A partial representation of the object model for DSOs being used at AtGDB. Customized features derived from distribution objects are shown in yellow. Solid lines represent object inheritance. The dashed line connecting the PlantGDB Unique Transcripts feature represents instantiation of the cDNA DSO. Grey objects represent federated adaptors to external resources. DSO, data source object.

A ZmGDB transcript view context page associated with the genomic region depicted in Figure 1. The feature graphic in the top window pane is described in Figure 1. Information at the top and left of this pane is displayed when passing the cursor over feature elements. Currently displayed is the information associated with the sixth intron (immediately left of the green viewfinder) of the GeneSeqer spliced alignment of a Zea mays cDNA sequence (accession AV109414, GenBank id 21213129). The vertical green bars represent the view finder for the sequence view found in the bottom window pane. Red nucleotides shown in this view represent alignment mismatches with the genomic sequence.

Individual feature pages found at AtGDB. (a) An AtGDB record page summarizing the GeneSeqer spliced alignment of an Arabidopsis thaliana cDNA sequence (accession BT020201, GenBank id 55733740). Feature structure glyphs found in the alignment loci summary table at the bottom of the window are as described in Figure 1. Green bars in the splice site distribution glyph represent the location of slice junctions in the processed mRNA transcript. (b) An AtGDB annotation record page detailing an Arabidopsis gene annotation (At3g15870.1). The GAEVAL Summary report at the bottom of the window displays information obtained using the integrated GAEVALxGDB services.