I have found that the plantdb database is quite useful in my work.
I have tried two different ways to annotate the transcription factors for my transcripts.
- Blastx my transcript sequences against protein sequences of All TFs in PlantTFDB 4.0.
- Use the functional module of Transcription Factor Prediction webserver to annotate the transcripts.
The results show that the two methods lead to two extremely different numbers of transcriptional factors (tens of thousands vs. hundreds).
I am wondering why they could result in so large differences and which one is better in practice? Why?
Many thanks for your help,