Greetings Arabidopsis researchers!
What's new in Araport
(1) We are pleased to announce the official release of the latest Arabidopsis genome reannotation effort “Araport11” (dated June 20, 2016). The Araport11 dataset is now available via ThaleMine, JBrowse, Downloads, and Science Apps. A draft manuscript describing the Araport11 annotation can be found at http://dx.doi.org/10.1101/047308.
- Araport Downloads, https://www.araport.org/downloads
- ThaleMine, https://apps.araport.org/thalemine/
- JBrowse, https://apps.araport.org/jbrowse/?data=arabidopsis
- Science Apps, https://www.araport.org/apps/catalog
NCBI GenBank has also accepted and made the Araport11 annotation public, accessible via the following URLs:
- NCBI (chromosome 1), http://www.ncbi.nlm.nih.gov/nuccore/CP002684
- NCBI (chromosome 2), http://www.ncbi.nlm.nih.gov/nuccore/CP002685
- NCBI (chromosome 3), http://www.ncbi.nlm.nih.gov/nuccore/CP002686
- NCBI (chromosome 4), http://www.ncbi.nlm.nih.gov/nuccore/CP002687
- NCBI (chromosome 5), http://www.ncbi.nlm.nih.gov/nuccore/CP002688
(2) We have added a new RNA-seq expression displayer to the ThaleMine Gene Report page, and RNA-seq read alignment tracks to JBrowse. The RNA-seq data collection contains 113 public datasets from 11 tissues.
Example quick links:
- ThaleMine Gene Report (ABI3/AT3G24650): http://www.araport.org/locus/AT3G24650
- JBrowse RNA-seq (ABI3/AT3G24650): http://www.araport.org/locus/AT3G24650/browse?tracks=Araport11_gene_mode...
Araport at ICAR 2016 (http://icar2016.arabidopsisresearch.org/icar2016/)
Come see Araport at ICAR 2016, South Korea (Talk, Araport Forum & Poster)
- Talk at Session 20 (Room 300C), Saturday July 2, 11.00am - 12.30pm (Chris Town)
- Araport Forum (Room 101, 102), Saturday July 2, 07.00pm - 08.30 pm (Araport, IAIC and community contributors)
- Poster (P535) in the New Technology session
About Araport (https://www.araport.org)
Araport aims to provide Arabidopsis and plant scientists direct access to a new generation web-based data platform. In a nutshell, users can browse and analyze a wide array of data through Araport, and can also publish their own modules for sharing data with the community or building analysis workflows. Araport also assumed the responsibility for updating and revising genome annotation (Araport11) and the reference genome sequence.
ThaleMine (https://apps.araport.org/thalemine/). A data warehouse for browsing gene reports, running gene list enrichment analysis, exporting data tables, and saving or sharing work.
JBrowse (https://apps.araport.org/jbrowse/?data=arabidopsis). A genome browser hosting close to 100 data tracks including population variant data from the 1001 Genomes Project. Users can also upload and view their own data for side-by-side comparison.
Science Apps (https://www.araport.org/apps/catalog). A growing collection of data or analysis modules that will serve as building blocks for creating discovery workflows.
Araport11 (https://www.araport.org/data/araport11). Comprehensive updates to Col-0 genome annotation including gene structures and functional annotation.
Tutorials (https://www.araport.org/tutorials). Video tutorials for assessing ThaleMine and JBrowse data.
For questions and comments, please contact email@example.com.
The Araport team
Araport is funded by the US National Science Foundation and the UK Biotechnology and Biological Sciences Research Council. Araport is a collaborative project started in 2013. Participating groups include J. Craig Venter Institute, Texas Advanced Computing Center, and the University of Cambridge.