Table 1 

Definitions of the different statistics. Definitions of the different statistics used. i and denote the sequence positions of a basepair in the known structure, c is an alternative pairing partner for i (but according to the basepairing rules therefore not for ), L is the length of the RNA sequence, N is the number of sequences in the data set and the index x indicates the type of weight used. Please refer to the text for a description of how alternative pairing partners are calculated. 

x 
p plain weights 
g free energy weights 


3'cis_{x} 
1/((c  i) log(L  i)) 
G_{ci}/((c  i) log(Li)) 
3'trans_{x} 
1/((c  ) log(L  )) 
G_{ci}/((c  ) log(L  )) 
5'cis_{x} 
1/((ic) log(i)) 
G_{ic}/((ic) log(i)) 
5'trans_{x} 
1/((  c)log()) 
G_{ic}/((  c) log()) 
cis_{x} 
5'cis_{x } 3'cis_{x} 

trans_{x} 
3'trans_{x } 5'trans_{x} 

3'Cis_{x} 
Σ_{#3'cis }3'cis_{x} 

3'Trans_{x} 
Σ_{#3'trans }3'trans_{x} 

5'Cis_{x} 
Σ_{#5'cis }5'cis_{x} 

5'Trans_{x} 
Σ_{#5'trans }5'trans_{x} 

Cis_{x} 
5'Cis_{x } 3'Cis_{x} 

Trans_{x} 
3'Trans_{x } 5'Trans_{x} 

where x ∈ {p,g}, y ∈ {3'Cis, 3'Trans, 5'Cis, 5'Trans, Cis, Trans} 



Meyer and Miklós BMC Molecular Biology 2004 5:10 doi:10.1186/14712199510 