发信人: Rizhard (Rizhard), 信区: Biology
标 题: Re: anyone working on RNA 2nd structure folding?
发信站: The unknown SPACE (Mon Aug 26 18:20:54 2002), 转信

你可以用Vienna Package
计算secondary structure的
partition function,这样就可疑
得到这个结构在所有可能构象中
所占的比利.Vienna Package is free online!
另外,mfold server也可以给出
次忧的结构,我个人认为次忧的结构
也可以看出最忧结构是否稳定.

【 在 tlbb (天龙下凡) 的大作中提到: 】
: that will tell me how good it is on a relatively value, but won't give me
: the answer i would like. Thanks anyway.
: 【 在 Tharu (待嫁的恐龙) 的大作中提到: 】
: : It really depends on the GC content of your RNA. My suggestion is to shuffle
: : and generate a random pool (say, 100) of your RNA based on the GC content.
: : Then run them through mfold (the server can handle batch jobs, you just need
: : to wait for a while), and then you will have a normal distribution of the
: : folding free energy. Compare the folding free energy of your native sequence
: : to the distribution will show you whether it's better or worse than random.


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