Your question as it is now is too incomplete and impossible to be answered in a meaningful way. Please read How To Ask Good Questions On Technical And Scientific Forums. What are your unigenes? An assembled transcriptome? ESTs?

But for question 1 (and assuming by "do gene ontology" you mean assign gene ontology categories to unigenes): homology searches using Blast and / or HMMER and annotation with Trinotate or other software.

Question 2: some papers indicate yes, you can use unigenes to find transcription factors - see examples here, here and here. As a bonus, the materials and methods from these papers will point to some solutions for your first question.