Introduction
SalmoBase is a comprehensive genomic data resource for Atlantic salmon and other salmonid species. It provides genome browsers, gene assemblies, and search tools, making molecular genomic resources for salmonids publicly available through integrated visualization and analysis frameworks. SalmoBase is the sister database of LiceBase.
Salmonids encompass 11 genera and at least 70 species, including Atlantic salmon, rainbow trout, whitefishes, graylings, and char. Their common ancestor experienced a whole genome duplication (WGD) approximately 80 million years ago, resulting in an autotetraploid genome. Ongoing genomic rediploidization makes salmonids a unique system for studying the evolutionary consequences of WGD.
Key Features
- Genome browser — browse salmonid species genomes interactively via JBrowse
- BLAST search — query salmonid genomic and protein sequences against reference databases
- SalMotifDB — access transcription factor binding motifs specific to salmonid species
- Gene assemblies — explore specific gene assemblies across multiple salmonid species
- High-quality references — includes established genome sequences for Atlantic salmon and rainbow trout
- Continuous updates — new genomic resources are added as they become publicly available
Getting Started
- Visit SalmoBase to explore available species and datasets
- Use the genome browser to navigate chromosomal regions of interest
- Run BLAST searches to find homologous sequences across salmonid genomes
- Access SalMotifDB for transcription factor binding site data