Protein-to-genome alignment with miniprot.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 36648328.
- Also identified by DOI 10.1093/bioinformatics/btad014 and PMC identifier 9869432.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over 10 years ago and did not incorporate the latest advances in alignment algorithms. They are inefficient and could not keep up with the rapid production of new genomes and quickly growing protein databases. Here, we describe miniprot, a new aligner for mapping protein sequences to a complete genome. Miniprot integrates recent techniques such as k-mer sketch and vectorized dynamic programming. It is tens of times faster than existing tools while achieving comparable accuracy on real data. https://github.com/lh3/miniport.
Medical subject headings
- Software
- Algorithms