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

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. -