Ensembl 'AlignView' is used to display sequence alignments for different purposes at various levels and in various formats.
Supporting Evidence Alignments - All Ensembl gene, transcript and protein model predictions are strongly based on direct experimental evidence. This biological evidence is imported via sequence records from public protein or nucleotide sequence databases and the 'Supporting Evidence' section on Ensembl 'ExonView' pages lists on a per exon basis, which records were used for the prediction of a particular transcript model. Clicking one of the exons leads to Ensembl 'AlignView' pages and allows for a direct comparison of Ensembl model predictions with the database sequence serving as the underlying biological evidence.
The following example illustrates an alignment of an Ensembl transcript exon to a UniProt/Swiss-Prot sequence.
Protein Family Alignments - For each release, Ensembl undertakes a huge effort to cluster all protein models of all species displayed in the genome browser into Ensembl protein families. Details upon Ensembl protein families, including a link to alignments of all members in 'AlignView' are available from Ensembl 'FamilyView' pages.
Orthologue Prediction Alignments - Ensembl aims to discover putatively orthologous genes in other species and lists them in 'Orthologue Prediction' sections on Ensembl 'GeneView' pages. [Align] links display a pairwise alignment of the gene currently viewed in 'GeneView' with the corresponding candidate in another species.
Conserved Blocks Alignments - Direct genome sequence comparisons reveal conserved DNA blocks shared between species. These DNA sequence blocks are annotated in the 'cons' and 'high cons' tracks on Ensembl 'ContigView' and 'MultiContigView' pages. Pointing with the mouse at one of these blocks in the ungrouped display mode brings up a pop-up window with 'Alignment' as the entry point to 'AlignView'.
The following multiple sequence alignment formats are currently supported:
- FASTA format
- MSF format
- ClustalW format
- Selex format
- PFAM format
- Mega format
- Nexus format
- Phylip format
- PSI format
The search box at the top of the page allows you to search for any identifier present in Ensembl. For detailed instructions see the Ensembl 'TextView' page.