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Next-Generation Sequence Databases: RNA and Genomic Informatics Resources for Plants

Mayumi Nakano, Kevin McCormick, Caghan Demirci, Feray Demirci, Sai Guna Ranjan Gurazada, Deepti Ramachandruni, Ayush Dusia, Joshua A Rothhaupt, Blake C. Meyers
Mayumi Nakano
Donald Danforth Plant Science Center CITY: St. Louis STATE: Missouri United States Of America [US]
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  • For correspondence: mnakano@danforthcenter.org
Kevin McCormick
University of Delaware CITY: Newark STATE: DE United States Of America [US]
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  • For correspondence: kevinmcc@pennmedicine.upenn.edu
Caghan Demirci
University of Delaware CITY: Newark STATE: DE United States Of America [US]
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  • For correspondence: caghan@udel.edu
Feray Demirci
Donald Danforth Plant Science Center CITY: St. Louis STATE: Missouri United States Of America [US]
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  • For correspondence: FDemirci@danforthcenter.org
Sai Guna Ranjan Gurazada
University of Delaware CITY: Newark STATE: DE United States Of America [US]
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  • For correspondence: guna.udel@gmail.com
Deepti Ramachandruni
University of Delaware CITY: Newark STATE: DE United States Of America [US]
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  • For correspondence: deepti.rs@gmail.com
Ayush Dusia
University of Delaware CITY: Newark STATE: DE United States Of America [US]
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  • For correspondence: adusia@udel.edu
Joshua A Rothhaupt
Donald Danforth Plant Science Center CITY: St. Louis STATE: Missouri United States Of America [US]
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  • For correspondence: jrothhaupt@danforthcenter.org
Blake C. Meyers
Donald Danforth Plant Science Center CITY: St. Louis STATE: Missouri POSTAL_CODE: 63132 United States Of America [US]
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  • For correspondence: bmeyers@danforthcenter.org

Published November 2019. DOI: https://doi.org/10.1104/pp.19.00957

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  • {copyright, serif} 2019 American Society of Plant Biologists. All rights reserved.

Abstract

We developed public websites and resources for data access, display, and analysis of plant small RNAs. These websites are interconnected with related data types. The current generation of these informatics tools was developed for Illumina data, evolving over >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 thaliana to wheat (Triticum sp.), 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 (PARE)/degradome reads, RNA-seq, and even chromatin immunoprecipitation (ChIP)-seq data; it also provides information about potentially novel transcripts (antisense transcripts, alternative splice isoforms, 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. -

  • Received August 6, 2019.
  • Accepted October 18, 2019.
  • Published November 5, 2019.

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RNA and Genomic Informatics Resources for Plants
Mayumi Nakano, Kevin McCormick, Caghan Demirci, Feray Demirci, Sai Guna Ranjan Gurazada, Deepti Ramachandruni, Ayush Dusia, Joshua A Rothhaupt, Blake C. Meyers
Plant Physiology Nov 2019, pp.00957.2019; DOI: 10.1104/pp.19.00957

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RNA and Genomic Informatics Resources for Plants
Mayumi Nakano, Kevin McCormick, Caghan Demirci, Feray Demirci, Sai Guna Ranjan Gurazada, Deepti Ramachandruni, Ayush Dusia, Joshua A Rothhaupt, Blake C. Meyers
Plant Physiology Nov 2019, pp.00957.2019; DOI: 10.1104/pp.19.00957
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Extras

  • First author profile: Mayumi Nakano

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Plant Physiology: 181 (4)
Plant Physiology
Vol. 181, Issue 4
Dec 2019
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