Salmobase
Updates
Update 2026-10-28
- Added assemblies:
- Arctic charr: Salp_Arthur
- Coho salmon: Okis_Carlos
- Danube salmon: Hhuc_Danny
- European grayling: Tthy_Gary
- Added assemblies of outgroup species:
- Northern pike: fEsoLuc1.pri
- Eastern mudminnow: UPYG_1.0
- Olympic mudminnow: Nhub_Marty
- New gene trees and orthologs including the new assemblies
- Updated Ensembl annotations to release 116.
- New version of SalmotifDB available!🎉
- Improved circos and synteny plots, with clearer colors and a legend for duplication resolution timing.
Earlier updates
Update 2025-09-11
- Added assembly: Arctic charr (fSalAlp1.1)
Update 2025-04-11
- Gene expression plot added to gene page
Update 2023-04-11
- "Genome browser" removed from menu. The genome browser can now be opened from the genome page by clicking on a chromosome or by select JBrowse from the tools menu.
- Link to download choromosomes.tsv on genome page.
- Added tracks:
- Comparative genome alignments for salmon and trout
- Comparative ortholog/paralog tracks
Update 2023-01-02:
- Added assemblies:
- Atlantic salmon: Ssal_Brian_v1.0
- Atlantic salmon: Ssal_ALTA
- Gene page now shows link between Ensembl and NCBI annotation
Correction 2022-12-05:
The assembly that was originally submitted as Arctic char (Salvelinus alpinus) has been corrected to Dolly Varden (Salvelinus malma). See this retraction notice.November 2022 Update:
- Added assemblies:
- Atlantic salmon: Ssal_v3.1
- Rainbow trout: USDA_OmykA_1.1
- Coho salmon: Okis_V2
- Now includes both NCBI and Ensembl annotations when available.
- Support for multiple assemblies per species (I.e. old assemblies are still available).
- Added filter for gene search: Search selected species, assembly or annotation.
- New gene trees and ortholog groups for the new species based on Ensembl annotations.
- Chromosome alias: Now possible to load tracks with alternative sequence names. Valid sequence IDs are. refseq, genbank, Ensembl or “sequence name”. Aliases are also displayed when hovering the chromosome on the genome page.
- Gene page URL now uses geneIDs by default (NCBI gene ID or Ensembl gene ID). Gene annotations from earlier assemblies can be accessed by specifying the assembly with a parameter. E.g. https://salmobase.org/genes/id/100306804?assembly=ICSASG_v2
About Salmobase
Salmobase brings salmonid genomes together with comparative analyses and functional datasets to help researchers explore gene function and genome evolution. Gene trees, ortholog groups, conserved gene order (synteny), and genome alignments connect genes and genomic regions across species and assemblies.
A particular focus is the legacy of the salmonid whole-genome duplication: identifying duplicated regions and exploring when duplicate copies began evolving independently. Interactive synteny views link this evolutionary context to individual genes and their surrounding regions.
Alongside NCBI and Ensembl references, Salmobase provides additional assemblies and annotations contributed by research groups. Gene pages and genome-browser tracks bring together expression data, regulatory annotations, and comparative results, making it easier to interpret a gene in its functional and evolutionary context.
Feedback
We appreciate your feedback! Please report any issues with the site or suggest a new feature or dataset you would like to see here by sending an e-mail
Features
Gene details
Shows gene annotation and structure. View and navigate between orthologs in the gene tree or synteny visualisation.
Example
Jbrowse2 genome browser
View gene annotations, orthologs, genome alignments as well as your own local track files (bigwig,bed,bam,gff,etc..).
BLAST search
Search for genomic, transcript or protein sequences within an assembly.
