As of Ensembl release 2026-07, you can explore genomic variation, including complex structural variants, between two assemblies using the Alignments viewer, compare DNA or protein sequences across genomes with the BLAST tool and use the Ensembl Variant Effect Predictor (VEP) to predict the molecular consequences of your own variants:

BLAST

The BLAST tool is a sequence similarity search tool for comparing DNA or protein sequences. Start by selecting a target database from the dropdown menu: DNA, transcripts, or proteins. The following BLAST algorithms are available in Ensembl:

• BLASTn – nucleotide sequence against a nucleotide database
• tBLASTn – translated nucleotide sequence against a nucleotide database
• tBLASTx – translated nucleotide sequence against a translated nucleotide database
• BLASTp – protein sequence against a protein database
• BLASTx – translated nucleotide sequence against a protein database

Alignments viewer

The Ensembl Alignments viewer allows intuitive investigation of haplotype-specific variation, including complex/structural regions. 

Ensembl VEP

Ensembl VEP predicts the molecular effects of genetic variants, including SNPs and structural variants, on genes, transcripts, proteins, and regulatory regions. You can input your variant coordinates and nucleotide changes to identify:

• Affected genes and transcripts
• Variant location
• Predicted molecular consequences (such as missense, stop gained, stop lost, or frameshift)