Using TRANSFAC .

Question

[yunnogal]

HI~ I am working on HPV viral genome sequence. I tried to find out the "putative transcription factor binding site" using TRANSFAC. BUT, I simply don't know how to use it. I put the FASTA sequence of the viral genome and ran TRANSFAC and start position, core match, matrix match and etc. What would be the limits of core match and matrix match that usually are considered as of significance? For example, I have transcription factor EV-1 binding site that has core match of 0.773 and matrix match of 0.649. Do you consider it of significance?

Please, I am desperate!! I am not a bioinformatician and it is really difficult for me to understand these~

HELP me on using TRANSFAC!

Thank you~

[zizigolu]

Don't worry friend, everything will be done well

Just insist on asking your question in biostar, you will get your answer!

[zizigolu]

Could you finally interpret TRANSFAC result? Do you know how I can visualise of the resulted matrix?

Answer 1

[cdsouthan]

Don't use it. You are better off looking for an HPV resource that compares the genome strains for conservation patches indicative of regulatory elements