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Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms

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 acc...

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Autores principales: Nord, Alexander J., Wheeler, Travis J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10166558/
https://www.ncbi.nlm.nih.gov/pubmed/37155621
http://dx.doi.org/10.1371/journal.pone.0285225
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author Nord, Alexander J.
Wheeler, Travis J.
author_facet Nord, Alexander J.
Wheeler, Travis J.
author_sort Nord, Alexander J.
collection PubMed
description 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.
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spelling pubmed-101665582023-05-09 Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms Nord, Alexander J. Wheeler, Travis J. PLoS One Research Article 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. Public Library of Science 2023-05-08 /pmc/articles/PMC10166558/ /pubmed/37155621 http://dx.doi.org/10.1371/journal.pone.0285225 Text en © 2023 Nord, Wheeler https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Nord, Alexander J.
Wheeler, Travis J.
Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms
title Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms
title_full Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms
title_fullStr Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms
title_full_unstemmed Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms
title_short Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms
title_sort mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10166558/
https://www.ncbi.nlm.nih.gov/pubmed/37155621
http://dx.doi.org/10.1371/journal.pone.0285225
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