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...

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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
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Abstract	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.
AbstractList	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.MOTIVATIONProtein-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.RESULTSHere, 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.AVAILABILITY AND IMPLEMENTATIONhttps://github.com/lh3/miniport. 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. 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. 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.
Author	Li, Heng
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Snippet	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... 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... 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...
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SubjectTerms	Algorithms Alignment Dynamic programming Gene mapping Gene sequencing Genome Genomes Original Paper Peptide mapping Proteins Sequence Alignment Sequence Analysis, DNA - methods Software
Title	Protein-to-genome alignment with miniprot
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