miniprot

miniprot aligns protein sequences to genomic DNA to annotate protein-coding genes and to detect splicing and frameshift events.

Key Features:

• Affine gap penalty, splicing and frameshift support: Employs an affine gap penalty model with explicit handling of splicing and frameshifts to improve protein-to-genome mapping.
• K-mer sketching: Uses k-mer sketching for efficient preprocessing and candidate selection from genomic data.
• Vectorized dynamic programming: Implements vectorized dynamic programming to accelerate alignment computations.
• High speed with comparable accuracy: Reported to be tens of times faster than previous alignment tools while maintaining comparable accuracy on real datasets.
• Optimization for modern computational environments: Incorporates algorithmic optimizations targeted to contemporary CPU/vector architectures.

Scientific Applications:

• Gene annotation in new and non-model species: Facilitates annotation of protein-coding genes by aligning known proteins from other organisms to target genomes.
• Functional genome annotation: Supports transfer of protein evidence to delineate exon–intron structures for functional annotation.
• Splicing and frameshift analysis: Enables identification of splicing patterns and frameshift events that affect gene structure and coding potential.

Methodology:

Uses k-mer sketching for preprocessing, vectorized dynamic programming for accelerated alignment, and an affine gap penalty model with explicit splicing and frameshift handling.