Division of labour
Data Curation: Li Zhang, Housong Cui, Runmao Lin
Web Development: Li Zhang, Housong Cui, Song Yu, Renlan Yan, Runmao Lin
Conceptualization: Bao Wang, Tong Liu
Design: Runmao Lin, Tong Liu
Contact us
We would love to hear from you for any questions or comments. Please find our contact information here.
E-mail: Fungalgenomics@163.com
If you use TGP-WEB for gene prediction analysis, please cite:
1. TGP-WEB (https://www.fungalgenomics.cn/geneprediction/)
Zhang L, Cui H, Yu S, Yan R, Wang B, Lin R, Liu T. TGP-WEB: A server for automatic gene prediction of Trichoderma genomes. Phytopathology. 2026. Online. doi: 10.1094/PHYTO-12-25-0399-R.
2. Augustus
Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., and Morgenstern, B. 2006. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34:W435-9.
3. GeneMark-ETP
Brůna, T., Lomsadze, A., and Borodovsky, M. 2024. GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes. Genome Res. 34:757-768.
4. Braker
Gabriel, L., Brůna, T., Hoff, K. J., Ebel, M., Lomsadze, A., Borodovsky, M., and Stanke, M. 2024. BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA. Genome Res. 34:769-777.
5. Prothint (https://github.com/gatech-genemark/ProtHint)
6. Pfam
Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E. L. L., Tosatto, S. C. E, Paladin, L., Raj, S., Richardson, L. J., Finn, R. D., and Bateman, A. 2021. Pfam: The protein families database in 2021. Nucleic Acids Res. 49:D412-D419.
7. NCBI refseq genes of fungi (https://ftp.ncbi.nlm.nih.gov/refseq/release/fungi/)
8. InParanoid
Persson, E., and Sonnhammer, E. L. L. 2023. InParanoiDB 9: Ortholog Groups for Protein Domains and Full-Length Proteins. J Mol Biol. 435:168001.
9. OrthoFinder
Emms, D. M., and Kelly, S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20:238.
Data privacy notice: Uploaded data is kept private, stored for one month, and then automatically deleted. TGP-WEB only hosts and displays publicly available genomic data from databases like NCBI.