{"title":"mapPat：追踪病原体在空间和时间上的进化。","authors":"Erika Ferrandi, Graziano Pesole, Matteo Chiara","doi":"10.1093/bioadv/vbaf015","DOIUrl":null,"url":null,"abstract":"<p><strong>Motivation: </strong>The COVID-19 pandemic highlighted the importance of genomic surveillance for monitoring pathogens evolution, mitigating the spread of infectious disorders, and informing decision-making by public health authorities. Since the need for the summarization and interpretation of large bodies of data, computational methods are critical for the implementation of effective genomic surveillance strategies.</p><p><strong>Results: </strong>Here, we introduce mapPat, an R Shiny application for the interactive visualization of pathogens genomic data in space and time. mapPat is designed as a user-friendly dashboard and allows the dynamic monitoring of the evolution of variants, lineages, and mutations in the genome of a pathogen at glance through informative geographic maps and elegant data visuals. mapPat provides a fine-grained map of pathogens evolution and circulation and represents a useful addition to the catalogue of bioinformatics methods for the genomic surveillance of pathogens.</p><p><strong>Availability and implementation: </strong>mapPat is available at GitHub (https://github.com/F3rika/mapPat.git).</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"5 1","pages":"vbaf015"},"PeriodicalIF":2.4000,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11835230/pdf/","citationCount":"0","resultStr":"{\"title\":\"mapPat: tracking pathogens evolution in space and time.\",\"authors\":\"Erika Ferrandi, Graziano Pesole, Matteo Chiara\",\"doi\":\"10.1093/bioadv/vbaf015\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Motivation: </strong>The COVID-19 pandemic highlighted the importance of genomic surveillance for monitoring pathogens evolution, mitigating the spread of infectious disorders, and informing decision-making by public health authorities. Since the need for the summarization and interpretation of large bodies of data, computational methods are critical for the implementation of effective genomic surveillance strategies.</p><p><strong>Results: </strong>Here, we introduce mapPat, an R Shiny application for the interactive visualization of pathogens genomic data in space and time. mapPat is designed as a user-friendly dashboard and allows the dynamic monitoring of the evolution of variants, lineages, and mutations in the genome of a pathogen at glance through informative geographic maps and elegant data visuals. mapPat provides a fine-grained map of pathogens evolution and circulation and represents a useful addition to the catalogue of bioinformatics methods for the genomic surveillance of pathogens.</p><p><strong>Availability and implementation: </strong>mapPat is available at GitHub (https://github.com/F3rika/mapPat.git).</p>\",\"PeriodicalId\":72368,\"journal\":{\"name\":\"Bioinformatics advances\",\"volume\":\"5 1\",\"pages\":\"vbaf015\"},\"PeriodicalIF\":2.4000,\"publicationDate\":\"2025-02-07\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11835230/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Bioinformatics advances\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1093/bioadv/vbaf015\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q2\",\"JCRName\":\"MATHEMATICAL & COMPUTATIONAL BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics advances","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioadv/vbaf015","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
mapPat: tracking pathogens evolution in space and time.
Motivation: The COVID-19 pandemic highlighted the importance of genomic surveillance for monitoring pathogens evolution, mitigating the spread of infectious disorders, and informing decision-making by public health authorities. Since the need for the summarization and interpretation of large bodies of data, computational methods are critical for the implementation of effective genomic surveillance strategies.
Results: Here, we introduce mapPat, an R Shiny application for the interactive visualization of pathogens genomic data in space and time. mapPat is designed as a user-friendly dashboard and allows the dynamic monitoring of the evolution of variants, lineages, and mutations in the genome of a pathogen at glance through informative geographic maps and elegant data visuals. mapPat provides a fine-grained map of pathogens evolution and circulation and represents a useful addition to the catalogue of bioinformatics methods for the genomic surveillance of pathogens.
Availability and implementation: mapPat is available at GitHub (https://github.com/F3rika/mapPat.git).
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