Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms
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Department of Pharmacology & Toxicology, University of ArizonaIssue Date
2023-05-08
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Nord AJ, Wheeler TJ (2023) Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms. PLoS ONE 18(5): e0285225. https://doi.org/10.1371/journal.pone.0285225Journal
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© 2023 Nord, Wheeler. This is an open access article distributed under the terms of the Creative Commons Attribution License.Collection Information
This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.Abstract
The organization of homologous protein sequences into multiple sequence alignments (MSAs) is a cornerstone of modern analysis of proteins. Recent focus on the importance of alternatively-spliced isoforms in disease and cell biology has highlighted the need for MSA software that can appropriately account for isoforms and the exon-length insertions or deletions that isoforms may have relative to each other. We previously developed Mirage, a software package for generating MSAs for isoforms spanning multiple species. Here, we present Mirage2, which retains the fundamental algorithms of the original Mirage implementation while providing substantially improved translated mapping and improving several aspects of usability. We demonstrate that Mirage2 is highly effective at mapping proteins to their encoding exons, and that these protein-genome mappings lead to extremely accurate intron-aware alignments. Additionally, Mirage2 implements a number of engineering improvements that simplify installation and use. © 2023 Nord, Wheeler. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Note
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1932-6203PubMed ID
37155621Version
Final Published Versionae974a485f413a2113503eed53cd6c53
10.1371/journal.pone.0285225
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Except where otherwise noted, this item's license is described as © 2023 Nord, Wheeler. This is an open access article distributed under the terms of the Creative Commons Attribution License.
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