PlantDeepSEA
Predicting Regulatory Effect of Genomic Variants
PlantDeepSEA is a webserver based on deep learning models of chromatin accessibility for multiple plant species. It can predict the impact of genomic variants on chromatin accessibility in multiple tissues. Therefore, it can be used to prioritize genomic variants and discover high-impact cis-regulatory sites within a sequence. PlantDeepSEA is freely accessible for all users.
Citation: Hu Zhao#, Zhuo Tu#, Yinmeng Liu, Zhanxiang Zong, Jiacheng Li, Hao Liu, Feng Xiong, Jinling Zhan, Xuehai Hu and Weibo Xie* (2021). PlantDeepSEA, a deep learning-based web service to predict the regulatory effects of genomic variants in plants. Nucleic Acids Research, doi: 10.1093/nar/gkab383
Trained models
Arabidopsis
Col-0
A small flowering plant that is widely used as a model organism in plant biology.
Rice
Brachypodium
Bd21
A model plant for temperate grasses and herbaceous energy crops.
Foxtail millet
Yuguyihao
An important grain crop as well as forage.
Sorghum
JDXBR
A biofuel crop and potential cellulosic feedstock.
Maize
B73
A staple food in many parts of the world.
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What's New
2021-06-04
Due to security concerns, now you can only submit 15 predictions in one hour.
2021-05-25
PlantDeepSEA has been published by Nucleic Acids Research.
2021-03-02
The rice model supports coordinates and intervals of multiple reference genomes.
2021-01-19
'Sequence Profiler' can accept input of a custom sequence for analysis.
2020-11-18
The online service of the Plant Multi-species Deep Learning Model is now available!