Category: Genes & Genomes: Bioinformatics
Araport (https://www.araport.org) aims to to provide a one-stop data platform for Arabidopsis and plant scientists. In Araport, users can search, analyze, and download a wide array of data through the core components ThaleMine and JBrowse. Araport has also released an extensive annotation update, Araport11, for the Col-0 reference genome.
ThaleMine is a powerful data warehouse for browsing the latest genome annotation from Araport11, integrated with RNA-seq expression, coexpression, physical and genetic interactions, pathways, seed stocks, publications, and more. ThaleMine also provides a user-friendly interface for running gene list enrichment analysis, building data queries, exporting data tables, and saving/sharing work. Araport11 is a comprehensive annotation update for both gene models and functional assignments using over 100 public RNA-seq datasets. The update included validating and adding splice isoforms, as well as genomic features such as novel transcribed regions, non-coding gene classes, upstream open reading frames (uORFs), and pseudogenes.
To further enhance data sharing by community members using Araport, the next phase of the project will include developing simple mechanisms for users to automatically integrate their data sets (including metadata) with Araport for easy sharing, discovery and reuse by other researchers. For example, users would be able to create data tracks in the Araport JBrowse for public sharing (e.g. RNA-seq alignments or expression profiles, community genome annotation, other genomic features), simply by providing the appropriate GFF or BAM file along with its associated metadata.
Araport is supported by the NSF and the BBSRC.
Agnes Chan– Assistant Professor, J Craig Venter Institute, Rockville, Maryland