Dear Biostars, Hi ('m not native in English)
I have seen in some papers that via blasting the assembled transcriptome against some TF database, the authors have found the Transcription factor (TFs) of their (non-model) species.
here are my questions :
1) Is this approach (finding TFs from RNA-seq datas) practical ? wouldn't the TF binding sites be in promoter regions and therefore likely not be in the expressed portion that RNA-seq have sequenced?
2) if (1) is practical, which kind of blast (-query is de novo transcriptome assembly) is better ? blastX or TBLASTN?
3) I want to discover the sex-biased TFs (something same as this). I have the DEGs between two sexes. Can I use the Blast and TF database of a model organism and my DEGs as query to discover differentially expressed Transcription factors ?
Thank you for sharing your knowledge