Sequence Similarity Search
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Introduction
Sequence Similarity Search searches CapBase nucleotide databases directly in the browser using minimap2 compiled to WebAssembly through Aioli/Biowasm. Paste or upload nucleotide FASTA queries, choose a Capsella genome and database, then run the alignment locally.
Available Databases
- Genome: searches the complete genome assembly, including intergenic regions.
- Gene genomic regions: searches genomic gene sequences that may include introns.
- Transcripts: searches annotated spliced transcript sequences.
- Coding sequences: searches annotated CDS sequences.
- Transposable elements: searches annotated TE copies.
Privacy
Searches run locally in your browser. Query sequences are not uploaded to CapBase.
Limitations
- This tool is powered by minimap2 and is not NCBI BLAST.
- The current version accepts nucleotide queries only.
- Short sequences may behave differently from BLASTN-short.
- Results depend on minimap2 heuristics, the selected preset, and the selected database.
- Large searches may require substantial browser memory because minimap2 indexes are large.
- Desktop browsers are recommended.
Citation
If you use this search tool, please cite minimap2:
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34:3094-3100. doi: 10.1093/bioinformatics/bty191.
The browser execution layer uses Aioli/Biowasm, which provides WebAssembly builds of bioinformatics command-line tools.