Mauve Viewer displays genomic features from annotation files overlaid on genome panels. This page describes how features are rendered, what information is available on hover and click, and how contig boundaries are shown.
When you load annotation files (GenBank, EMBL, or INSDseq XML) alongside an alignment, features appear as colored boxes on the genome panels:
| Feature Type | Color |
|---|---|
| CDS (Coding Sequence) | White |
| gene | White |
| tRNA | Green |
| rRNA | Red |
| misc_RNA | Blue |
Features on the forward strand appear above the center line. Features on the reverse strand are shifted below the center line.
Annotations are only displayed when the visible region is smaller than 1 Mbp (one million base pairs). Zoom in further to see individual features. This threshold prevents the display from becoming cluttered at wide zoom levels.
Hover over a feature to see a tooltip with:
- Feature type
- Locus tag
- Gene name
- Product description
- Genomic coordinates (start–end)
- Strand direction
Click on a feature to open a detail popup with full annotation information. The popup includes clickable links to external databases when available.
If the feature has a protein_id qualifier, the popup includes a link to the NCBI protein record.
db_xref qualifiers (format: Database:ID) are resolved to clickable hyperlinks. Multiple cross-references in a single qualifier are separated by semicolons; each recognized entry is rendered as a separate link.
| Database prefix | Link destination |
|---|---|
GeneID |
NCBI Gene |
UniProtKB |
UniProt |
UniProtKB/Swiss-Prot |
UniProt |
UniProtKB/TrEMBL |
UniProt |
PDB |
RCSB Protein Data Bank |
GO |
EBI QuickGO |
InterPro |
EBI InterPro |
KEGG |
KEGG (identifier must match organism:entry format, e.g. eco:b0001) |
Unrecognized database prefixes are silently ignored. Links open in a new browser tab. The raw db_xref text is not shown separately when cross-reference links are rendered.
When a genome contains multiple contigs (sequence records), red vertical lines mark the boundaries between contigs. You can toggle contig boundary display with the "Show Contigs" option.
Annotations are loaded lazily: they are fetched and parsed only when needed, and cached for subsequent views. This keeps the initial load fast even when annotation files are large.