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Next-Generation Sequence Databases: RNA and Genomic Informatics Resources for Plants.
Nakano, Mayumi; McCormick, Kevin; Demirci, Caghan; Demirci, Feray; Gurazada, Sai Guna Ranjan; Ramachandruni, Deepti; Dusia, Ayush; Rothhaupt, Joshua A; Meyers, Blake C.
Afiliación
  • Nakano M; Donald Danforth Plant Science Center, St. Louis, Missouri 63132.
  • McCormick K; Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711.
  • Demirci C; Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711.
  • Demirci F; Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711.
  • Gurazada SGR; Donald Danforth Plant Science Center, St. Louis, Missouri 63132.
  • Ramachandruni D; Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711.
  • Dusia A; Donald Danforth Plant Science Center, St. Louis, Missouri 63132.
  • Rothhaupt JA; Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711.
  • Meyers BC; Donald Danforth Plant Science Center, St. Louis, Missouri 63132.
Plant Physiol ; 182(1): 136-146, 2020 01.
Article en En | MEDLINE | ID: mdl-31690707
We developed public web sites and resources for data access, display, and analysis of plant small RNAs. These web sites are interconnected with related data types. The current generation of these informatics tools was developed for Illumina data, evolving over more than 15 years of improvements. Our online databases have customized web interfaces to uniquely handle and display RNA-derived data from diverse plant species, ranging from Arabidopsis (Arabidopsis thaliana) to wheat (Triticum spp.), including many crop and model species. The web interface displays the abundance and genomic context of data for small RNAs, parallel analysis of RNA ends/degradome reads, RNA sequencing, and even chromatin immunoprecipitation sequencing data; it also provides information about potentially novel transcripts (antisense transcripts, alternative splice isoforms, and regulatory intergenic transcripts). Numerous options are included for downloading data as tables or via web services. Interpretation of these data is facilitated by the inclusion of extensive repeat or transposon data in our genome viewer. We have developed graphical and analytical tools, including a new viewer and a query page for the analysis of phased small RNAs; these are particularly useful for understanding the complex small RNA pathways of plants. These public databases are accessible at https://mpss.danforthcenter.org.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Triticum / Arabidopsis / ARN de Planta / Genoma de Planta / Regulación de la Expresión Génica de las Plantas / Secuenciación de Nucleótidos de Alto Rendimiento Idioma: En Revista: Plant Physiol Año: 2020 Tipo del documento: Article Pais de publicación: Estados Unidos
Texto completo
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PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Triticum / Arabidopsis / ARN de Planta / Genoma de Planta / Regulación de la Expresión Génica de las Plantas / Secuenciación de Nucleótidos de Alto Rendimiento Idioma: En Revista: Plant Physiol Año: 2020 Tipo del documento: Article Pais de publicación: Estados Unidos