Protein-to-genome alignment with miniprot.

Area of Science:

• Genomics
• Bioinformatics

Background:

• Protein-to-genome alignment is essential for gene annotation, especially in non-model organisms.
• Existing tools are outdated, inefficient, and struggle with large-scale genomic and protein data.

Purpose of the Study:

• To introduce miniprot, a novel and efficient protein-to-genome alignment tool.
• To address the limitations of current alignment software in terms of speed and scalability.

Main Methods:

• Miniprot integrates k-mer sketching for rapid candidate identification.
• It employs vectorized dynamic programming for accurate sequence alignment.
• The tool is designed for high-throughput analysis of large genomic and protein datasets.

Main Results:

• Miniprot demonstrates a speed increase of tens of times compared to existing tools.
• It achieves comparable accuracy to established methods on real-world data.
• The new aligner effectively handles the rapid growth of genomic and protein databases.

Conclusions:

• Miniprot offers a significant advancement in protein-to-genome alignment efficiency.
• It provides a scalable solution for gene annotation in the era of big genomic data.
• The tool is readily available for researchers to enhance their annotation pipelines.