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Miniprot

Definition
AI-generated

Miniprot is a fast aligner that maps protein sequences to a genome while allowing splice boundaries, analogous to spliced aligners for transcripts.

Topics
Post-GWAS
URL
https://github.com/lh3/miniprot
Related
EviAnn Genome Annotation LiftOn

Why it matters in GWAS

Protein-level evidence strengthens gene models in new assemblies and pangenome graphs; consistent CDS boundaries matter for coding consequence calls when annotators use miniprot or related tools (e.g. within GALBA or LiftOn workflows).

Example usage

"We aligned UniProt proteins with miniprot to supplement RNA-seq evidence in the automated annotation."

EviAnn Genome Annotation LiftOn Transcript Assembly
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Li H. (2023). Protein-to-genome alignment with miniprot. Bioinformatics.
  • Ji HJ, Pertea M, Salzberg SL. (2026). Annotating genomes at increased scale and resolution. Nat Rev Genet. https://doi.org/10.1038/s41576-026-00937-3
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