دورية أكاديمية
happi: a hierarchical approach to pangenomics inference.
| العنوان: | happi: a hierarchical approach to pangenomics inference. |
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| المؤلفون: | Trinh P; Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA, USA., Clausen DS; Department of Biostatistics, University of Washington, Seattle, WA, USA., Willis AD; Department of Biostatistics, University of Washington, Seattle, WA, USA. adwillis@uw.edu. |
| المصدر: | Genome biology [Genome Biol] 2023 Sep 29; Vol. 24 (1), pp. 214. Date of Electronic Publication: 2023 Sep 29. |
| نوع المنشور: | Journal Article; Research Support, N.I.H., Extramural |
| اللغة: | English |
| بيانات الدورية: | Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: London, UK : BioMed Central Ltd Original Publication: London : Genome Biology Ltd., c2000- |
| مواضيع طبية MeSH: | Metagenomics* , Microbiota*/genetics, Metagenome ; Computer Simulation ; Sequence Analysis, DNA |
| مستخلص: | Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable and non-culturable microorganisms. However, metagenome-assembled genomes vary in quality and may contain omissions and contamination. These errors present challenges for detecting genes and comparing gene enrichment across sample types. To address this, we propose happi, an approach to testing hypotheses about gene enrichment that accounts for genome quality. We illustrate the advantages of happi over existing approaches using published Saccharibacteria MAGs, Streptococcus thermophilus MAGs, and via simulation. (© 2023. BioMed Central Ltd., part of Springer Nature.) |
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| معلومات مُعتمدة: | R21 AI168679 United States AI NIAID NIH HHS; R35 GM133420 United States GM NIGMS NIH HHS; T32 ES015459 United States ES NIEHS NIH HHS |
| فهرسة مساهمة: | Keywords: Hypothesis testing; Metagenome-assembled genomes; Microbiome; Shotgun metagenomics; Statistical models |
| تواريخ الأحداث: | Date Created: 20230929 Date Completed: 20231002 Latest Revision: 20240129 |
| رمز التحديث: | 20240129 |
| مُعرف محوري في PubMed: | PMC10540326 |
| DOI: | 10.1186/s13059-023-03040-6 |
| PMID: | 37773075 |
| قاعدة البيانات: | MEDLINE |
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Full Text Finder | تدمد: | 1474-760X |
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| DOI: | 10.1186/s13059-023-03040-6 |