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Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes
https://oist.repo.nii.ac.jp/records/2739
https://oist.repo.nii.ac.jp/records/27399cb66963-6100-44fa-bb14-728a6fd2348c
名前 / ファイル | ライセンス | アクション |
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Syberg-Olsen-2022-Pseudofinder_ Detection of P_vor (573.6 kB)
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CC BY 4.0
Creative Commons Attribution 4.0 International (https://creativecommons.org/licenses/by/4.0/) |
Item type | 学術雑誌論文 / Journal Article(1) | |||||
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公開日 | 2022-08-08 | |||||
タイトル | ||||||
言語 | en | |||||
タイトル | Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes | |||||
言語 | ||||||
言語 | eng | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | dN/dS | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | bacteria | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | archaea | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | genome | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | pseudogene | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | annotation | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | prediction | |||||
資源タイプ | ||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
資源タイプ | journal article | |||||
著者(英) |
Syberg-Olsen, Mitchell J
× Syberg-Olsen, Mitchell J× Garber, Arkadiy I× Keeling, Patrick J× McCutcheon, John P× Husnik, Filip |
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書誌情報 |
en : Molecular Biology and Evolution 巻 39, 号 7, p. msac153, 発行日 2022-07-08 |
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抄録 | ||||||
内容記述タイプ | Other | |||||
内容記述 | Prokaryotic genomes are usually densely packed with intact and functional genes. However, in certain contexts, such as after recent ecological shifts or extreme population bottlenecks, broken and nonfunctional gene fragments can quickly accumulate and form a substantial fraction of the genome. Identification of these broken genes, called pseudogenes, is a critical step for understanding the evolutionary forces acting upon, and the functional potential encoded within, prokaryotic genomes. Here, we present Pseudofinder, an open-source software dedicated to pseudogene identification and analysis in bacterial and archaeal genomes. We demonstrate that Pseudofinder’s multi-pronged, reference-based approach can detect a wide variety of pseudogenes, including those that are highly degraded and typically missed by gene-calling pipelines, as well newly formed pseudogenes containing only one or a few inactivating mutations. Additionally, Pseudofinder can detect genes that lack inactivating substitutions but experiencing relaxed selection. Implementation of Pseudofinder in annotation pipelines will allow more precise estimations of the functional potential of sequenced microbes, while also generating new hypotheses related to the evolutionary dynamics of bacterial and archaeal genomes. | |||||
出版者 | ||||||
出版者 | Oxford University Press | |||||
出版者 | ||||||
出版者 | Society for Molecular Biology and Evolution | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 0737-4038 | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 1537-1719 | |||||
PubMed番号 | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | PMID | |||||
関連識別子 | info:pmid/35801562 | |||||
DOI | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | DOI | |||||
関連識別子 | info:doi/10.1093/molbev/msac153 | |||||
権利 | ||||||
権利情報 | © 2022 The Author(s). | |||||
関連サイト | ||||||
識別子タイプ | URI | |||||
関連識別子 | https://academic.oup.com/mbe/article/39/7/msac153/6633826 | |||||
著者版フラグ | ||||||
出版タイプ | VoR | |||||
出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 |