HI Sam

Thanks for your help yesterday. The sequence I have is

GGGAGAGGGUUUAAUCUGUACGAAAGUACUGAUUGGAUCCGCAAGG

with constraint as

......((((((((((.((((....)))).))))))))))......

 

I generated the secondary structure using Vienna RNA server and I saved the file format in .ct format. I was wondering is there any utility which helps you to convert .ct format to .dat format?

or you have to manually modify the dat file. for example in my case I will have to specify the watson crick base pairing begining for 7th base with the 43th base and continue on.  Is this correct?

Regards

Raman

On 3 March 2010 21:00, Raman Parkesh <rparkesh@gmail.com> wrote:

HI 

thanks my number is

regards

Raman

On 3 March 2010 20:58, Samuel Coulbourn Flores <scflores@stanford.edu> wrote:

call me again .. i hung up accidentally

also maybe you should give me your number

sam

On Mar 2, 2010, at 7:14 PM, Raman Parkesh wrote:

Dear Prof.Coulbourn

I was trying your tutorial for RNABuilder. I am writing you to request for some information about how you can generate  the following files from RNA secondary structures

Base-interactionparameters.

pseudoelectrostatic.csv and

contacts.singlebasepair.1.dat

Your help will be appreciated.

Regards

Raman