DeepLRR: An Online Webserver for Leucine-Rich-Repeat Containing Protein Characterization Based on Deep Learning
Abstract
:1. Introduction
2. Materials and Methods
2.1. DeepLRR Overview
2.2. LRR Positive Sample Dataset Construction
2.3. LRR Negative Sample Dataset Construction
2.4. Training, Validation and Testing Dataset
2.5. Input Matrix
2.6. CNN Model Structure
2.7. Model Training
2.8. Performance Evaluation
2.9. LRR Domain Prediction
2.10. Plant Disease Resistance Proteins and Non-Canonical Domains
2.11. Re-Annotation of LRR-RLK Genes in Arabidopsis, Rice and Tomato Genomes Based on DeepLRR
2.12. Chromosome Mapping, Gene Cluster Analysis and Phylogenetic Analysis
3. Results
3.1. Characterization of Highly Conserved Segment Pattern in LRR Units
3.2. Comparison of LRR Unit Prediction Performance for Different Models
3.3. Optimization of DeepLRR Parameters for LRR Domain Characterization
3.4. Comparison of DeepLRR Performance with Existing Tools on LRR Domain Characterization
3.5. Webserver Implementation
3.6. Re-Annotation of LRR-RLK Genes in Arabidopsis, Rice and Tomato Genomes
3.7. Chromosome Mapping, Gene Cluster Analysis and Phylogenetic Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Method | Precision | Sensitivity | F1 |
---|---|---|---|
LRRpredictor | 0.582 | 0.854 | 0.692 |
LRRsearch | 0.676 | 0.813 | 0.739 |
LRRfinder | 0.798 | 0.669 | 0.728 |
Pfam | 0.192 | 0.037 | 0.062 |
Prosite | 0.836 | 0.379 | 0.522 |
Smart | 0.398 | 0.167 | 0.235 |
DeepLRR | 0.744 | 0.783 | 0.763 |
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Liu, Z.; Ren, Z.; Yan, L.; Li, F. DeepLRR: An Online Webserver for Leucine-Rich-Repeat Containing Protein Characterization Based on Deep Learning. Plants 2022, 11, 136. https://doi.org/10.3390/plants11010136
Liu Z, Ren Z, Yan L, Li F. DeepLRR: An Online Webserver for Leucine-Rich-Repeat Containing Protein Characterization Based on Deep Learning. Plants. 2022; 11(1):136. https://doi.org/10.3390/plants11010136
Chicago/Turabian StyleLiu, Zhenya, Zirui Ren, Lunyi Yan, and Feng Li. 2022. "DeepLRR: An Online Webserver for Leucine-Rich-Repeat Containing Protein Characterization Based on Deep Learning" Plants 11, no. 1: 136. https://doi.org/10.3390/plants11010136