What's New - RiceVarMap

2020-05-10

We have developed a non-coding variation impact prediction tool in the "Regulatory Variant Prioritization" page. Users can use the variation IDs or upload a VCF file to query the predicted variation impacts in our database.

2019-08-01

We fixed "Haplotype Network Analysis" page, which is now available.

2019-05-15

Chromatin Accessibility Map and  Non-coding Varation Scores Map can be seached in "Search for Variation by Gene" page.

2019-04-28

we comprehensively integrated non-coding variant prediction scores into RiceVarMap based on chromatin accessibility (CA) data and deep convolutional neural networks (CNNs).

   We  generated high-quality CA data from six representative rice tissues and used these data to train CNNs (AUROC: 0.93-0.95)  to predict the impacts of variants on CA in non-coding regions.

2019-03-10

We changed the web-based genome browser from GBrowse to JBrowse, and its improvements in speed and scalability are accompanied by specific enhancements that support complex interactive queries on large sets of tracks.

2019-01-20

winkWe improved the speed of "Search for Genotype With Variation ID"and "Search for Cultivar Information" page.

2018-06-20

We defined a 'Chromatin Accessibility Score' for each variation to evaluate the impact of variations (especially for non-coding variations) based on chromatin accessibility data. This information can be found at 'Search for Variation by Gene' page and  'Search for Variation information by Variation ID' page.

2018-05-02

Gene expression atlas added into RiceVarMap, gene expression across the tissues and stages can be queried at "Search for Variation by Gene" page.

2018-04-20

We added callus, root, young leaf, flag leaf, and spikelet's chromatin accessibility data to RiceVarMap, which can be searched in "Search for Variation by Gene" page.

2017-10-08

Gene symbol and gene name like 'hwh1' can be searched in 'Search for Variation by Gene' page.

2017-09-05

RiceVarMap v2.0 has been released!

new genomic variations and GWAS results, improved annotations of missense variations, integrated chromatin accessibility data for non-coding variations.