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| Online Databases/Tools by Bioinplant Lab: |
| BreedingAIDB: A database integrating crop genome-to-phenotype paired data with machine learning tools applicable in breeding. Shen et al., 2024, Plant communications |
| planTrichome: A database of glandular trichome cells in plants. Chen et al., 2024, iScience |
| VarietyFace: A platform for crop variety genomes and breeding. |
| PscLncRNA: A database for plant single-cell lncRNA analysis. Xu et al., 2024, New Phytologist |
| The database of N3: plants,genomes,technologies. Xie et al., 2024, Nature Plant |
| PlantscRNAdb: A database for plant single-cell RNA analysis. Chen et al., 2021, Molecular Plant |
| PlantcircBase: A database for plant circular RNAs. Chu et al., 2017, Molecular Plant |
| BnPedigome: A genomic database for the pedigrees and breeding of Brassica napus. Zou et al., 2019, Plant Biotechnology Journal |
| RiceRelativesGD: A genomic database of rice relatives for rice breeding. Mao et al., 2019, Database |
| Local Software by Bioinplant Lab: |
| ePmiRNA_finder: Multi-layer feature selection methods and classifiers for plant-derived miRNA identification from animal miRNA sequencing data. . Chen et al., 2021, PLoS One |
| DipHiC: A pipeline for polyploid genome scaffolding using diploid ancestry information and HiC data . Wu et al., 2021, Nature Communications |
| Scan_phasiRNA: A program to find loci with 21nt phased siRNAs (such as ta-siRNA gene TAS) using the Howell algorithm (Download). Shen et al., 2009, Plant Systematics and Evolution |
| eTM_finder: A tool to predict eTMs (endogenous target mimics) of miRNAs in plants (Download). Ye et al., 2014, Frontiers in Plant Science |
| circseq-cup: A program to assemble full-length sequences of circular RNAs (Download). Ye et al., 2016, RNA Biology |
| PcircRNA-finder: A program to identify circular RNAs in plants (Download). Chen et al., 2016, Bioinformatics |
| circRNA_pocket: A tool to show genomic features of circRNAs (Download). Zhang et al., 2016, 已获得计算机软件著作权【Patent registration number：2017SR231288】 |
| TOD-Bayes: A naïve Bayes algorithm for tissue origin diagnosis of synchronous multifocal tumors in the hepatobiliary and pancreatic system (Download). 2017, International Journal of Cancer |
| Other Public Bioinformatic Tools: |
| DNATOOL |
| TREEView |
| PCGENE |
| CLUSTALX |
| GENDOC32 |
| PRIMER5 |
| QTLMapper_V1.6 |
| QTLNetwork 1.0 |
| WinQTLCart (V2.0) |
| GenScan |
| Sequin |
| Antheprot |
| Rasmol |
| Swiss-PDBViewer |
| Chromos2.13 |
| MEGA 5.05 |
| BioEdit |
| MAFFT |
| Notepad++ |
| TBtools |
| Blast |