![]() The list of annotation fields displayed in Geneious is derived from the imported reference genome file. The two annotation methods described here show a slightly different list of fields, so for a thorough analysis, you may want to examine both. Protein or enzyme product associated with annotation. ![]() Indicates the offset at which the first complete codon of a coding feature can be found, relative to the first base of that feature. Often synonymous with a gene name or gene symbol.ĭescription about the structure or function of genomic region. Unique identifier for a specific genomic region. Nucleotide bases associated with the annotation. Number of nucleotide bases, including gaps, associated with annotation. Number of nucleotide bases, excluding gaps, associated with annotation. NCBI ontology for describing genomic features. ![]() Name of genomic feature associated with annotation. Table 1 shows definitions of the various annotation fields. Conversely, you could restrict the displayed annotations to a single type, say, tRNA by only choosing tRNA in the “Types” list. For example, you could add annotations for rRNA and tRNA. You can add more regions by checking other “Types” in the Document Viewer right panel. The instructions described so far only list the annotations for CDS regions of the genome. The list box shows additional details about this particular annotation.Īs shown in Fig. In the popup box click “Properties” to display a list box.Double-click the first annotation to display a popup box “Edit annotation”.In the Document Viewer (center panel), click the “Annotations” tab.Here is another method for displaying annotation information: The fields in this popup box are described below. 2, if you hover the mouse pointer over the yellow highlighted genomic region, it displays a popup box with additional details about this particular annotation. ![]() The exact sequence of steps may vary somewhat from those shown here depending on your version of Geneious, your workstation operating system, and any prior existing configuration options you may have set in Geneious.Īs shown in Fig. In the Document Viewer (right panel), click “Zoom to selection” (two inward-facing blue arrows).Īt this step, the first listed annotation should be highlighted in blue (bottom panel) and the corresponding genomic region should be highlighted in yellow (center panel).Click the first annotation in the list to highlight it in blue.In the Annotation Table (bottom panel), click “Name” to sort the annotations alphabetically.In Annotations and Tracks, check “Show Annotations”, check “Types”, check “CDS”, uncheck all remaining tracks.In the Document Viewer (right panel), click the “Annotations and Tracks” tab (right yellow arrow).In the Document Viewer (center panel), click the “Contig View” tab.“demo_bacteria_geneious_R ( assembled to Staphylococcus aureus )” in our example). In the Document Table (top panel), check the contig file that contains the sequence alignment (i.e.To display the Geneious main window as shown in Fig. And we’ll assume you have navigated to the subdirectory that contains the results of the sequence alignment algorithm. Annotation is often used to describe the structure and function of various genomic regions, such as genes, CDS‘s (coding sequences), exons, introns, 5′- 3′- UTR‘s, tRNA‘s, rRNA‘s, ORF‘s (open-reading frames), etc.įor this article we’ll assume that you already have Geneious running on a local workstation, that you have imported a reference genome into Geneious, have imported a sample FastQ file, and have run a sequence alignment of the sample against the reference genome. Geneious Prime includes genome annotation features and reports.
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