Protein-to-genome alignment with miniprot

Abstract Motivation 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 k...

Full description

Saved in:
Bibliographic Details
Published in:Bioinformatics (Oxford, England) Vol. 39; no. 1
Main Author: Li, Heng
Format: Journal Article
Language:English
Published: England Oxford University Press 01.01.2023
Oxford Publishing Limited (England)
Subjects:
Algorithms
Alignment
Dynamic programming
Gene mapping
Gene sequencing
Genome
Genomes
Original Paper
Peptide mapping
Proteins
Sequence Alignment
Sequence Analysis, DNA - methods
Software
ISSN:1367-4811, 1367-4803, 1367-4811
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Abstract Motivation 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. Results 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. Availability and implementation https://github.com/lh3/miniport.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
content type line 23
ISSN:1367-4811
1367-4803
1367-4811
DOI:10.1093/bioinformatics/btad014