scholarly journals High-throughput sequencing-based genome-wide identification of microRNAs expressed in developing cotton seeds

2015 ◽  
Vol 58 (8) ◽  
pp. 778-786 ◽  
Author(s):  
YanMei Wang ◽  
Yan Ding ◽  
DingWei Yu ◽  
Wei Xue ◽  
JinYuan Liu
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genome Wide ◽  
Cotton Seeds

scholarly journals PRIME-3D2D is a 3D2D model to predict binding sites of protein–RNA interaction

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Juan Xie ◽  
Jinfang Zheng ◽  
Xu Hong ◽  
Xiaoxue Tong ◽  
Shiyong Liu
Keyword(s):  
Full Advantage ◽  
High Throughput ◽  
Binding Sites ◽  
High Throughput Sequencing ◽  
Secondary Structures ◽  
Biological Processes ◽  
Genome Wide ◽  
Rna Interaction ◽  
Rna Complexes ◽  
Better Than

AbstractProtein-RNA interaction participates in many biological processes. So, studying protein–RNA interaction can help us to understand the function of protein and RNA. Although the protein–RNA 3D3D model, like PRIME, was useful in building 3D structural complexes, it can’t be used genome-wide, due to lacking RNA 3D structures. To take full advantage of RNA secondary structures revealed from high-throughput sequencing, we present PRIME-3D2D to predict binding sites of protein–RNA interaction. PRIME-3D2D is almost as good as PRIME at modeling protein–RNA complexes. PRIME-3D2D can be used to predict binding sites on PDB data (MCC = 0.75/0.70 for binding sites in protein/RNA) and transcription-wide (MCC = 0.285 for binding sites in RNA). Testing on PDB and yeast transcription-wide data show that PRIME-3D2D performs better than other binding sites predictor. So, PRIME-3D2D can be used to predict the binding sites both on PDB and genome-wide, and it’s freely available.

scholarly journals Identification and integrated analysis of glyphosate stress-responsive microRNAs, lncRNAs, and mRNAs in rice using genome-wide high-throughput sequencing

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Rongrong Zhai ◽  
Shenghai Ye ◽  
Guofu Zhu ◽  
Yanting Lu ◽  
Jing Ye ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Integrated Analysis ◽  
Genome Wide

Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing

2020 ◽  
Vol 20 (6) ◽  
pp. 825-838
Author(s):  
Xiaoqian Liu ◽  
Shanshan Chu ◽  
Chongyuan Sun ◽  
Huanqing Xu ◽  
Jinyu Zhang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genome Wide ◽  
Low Phosphorus ◽  
Soybean Genotypes

Genome-Wide Identification of Embryogenesis-Associated microRNAs in Radish (Raphanus sativus L.) by High-Throughput Sequencing

2014 ◽  
Vol 32 (4) ◽  
pp. 900-915 ◽  
Author(s):  
Lulu Zhai ◽  
Liang Xu ◽  
Yan Wang ◽  
Danqiong Huang ◽  
Rugang Yu ◽  
...  
Keyword(s):  
High Throughput ◽  
Raphanus Sativus ◽  
High Throughput Sequencing ◽  
Genome Wide ◽  
Raphanus Sativus L
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