I tried to find the ftp site, but found the email address of Dr.Prestridge is not valid any more.
could you please tell me whether there are any user friendly software that I can use for promoter and protein binding sites analysis? Is there any software which can analyze the non-coding RNA or enhancer interaction with promoter?
There is a program Promoter Scan designed by D. Prestridge. This program
seek possible promoter sequences, estimating density of protein binding
sites (cis-acting elements) ( see J.Mol.Biol. 249, N.5:923-932 (1995)).
You can write D. Prestridge (e-mail: danpbiosci.umn.edu) and he will tell
you ftp site with this program.
Hope, it helps,