Please kindly let me know, the concepts of secondary structure prediction by using NCBI BLAST, HHpred and Jpred. Are they any links. My teacher gave me one sequence and by using these program, I need to search the domain. When will start and when will end. Firstly I used NCBI, secondly I used HHpred and then I use Jpred.I found PDZ doamin and checked the secondary structure at HHpred and Jpred , I got the same results. So I think this is the my target domain. I answer to my teacher. But my teacher asked me again, why do u think this is your PDZ domain? What is the evidence? How about the other you not think domain? etc., so many how??? and why??? . Actually I am not too familier with this , so I can not answer. But I have to gave answer to my teacher on tomorrow. So please share me your knowledge, suggestionas and ideas.
Thank you Pont