miniprot ☆
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Description:
Align proteins to genomes with splicing and frameshift
Type: Formula  |  Tracked Since: Dec 28, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics alignment genomics protein cli
Install: brew install miniprot
About:
Miniprot is an ultra-fast protein-to-genome aligner designed to handle splicing and frameshifts efficiently. It utilizes minimizers and dynamic programming to accurately map protein sequences against large genomes, making it ideal for gene annotation and evolutionary studies. The tool provides a lightweight alternative to traditional alignment pipelines with significantly improved speed.
Key Features:
  • Ultra-fast alignment of proteins to genomes
  • Robust handling of introns and frameshifts
  • Produces standard GFF3 output format
  • Low memory footprint and efficient resource usage
Use Cases:
  • Annotating novel genomes using protein homologs
  • Identifying gene structures and splice variants
  • Comparative genomics and evolutionary analysis
Alternatives:
  • GMAP – GMAP is a widely used long-read aligner but Miniprot is generally faster and more sensitive for protein-to-genome tasks.
  • Exonerate – Exonerate is a generic alignment tool that is more versatile but significantly slower than Miniprot for protein mapping.
Version History
Detected Version Rev Change Commit
Sep 15, 2025 10:44pm 0 VERSION_BUMP c7275d76
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