Table 1

Definitions of the different statistics. Definitions of the different statistics used. i and denote the sequence positions of a base-pair in the known structure, c is an alternative pairing partner for i (but according to the base-pairing 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'cisx

1/((c - i) log(L - i))

|Gci|/((c - i) log(L-i))

3'transx

1/((c - ) log(L - ))

|Gci|/((c - ) log(L - ))

5'cisx

1/((i-c) log(i))

|Gic|/((i-c) log(i))

5'transx

1/(( - c)log())

|Gic|/(( - c) log())

cisx

5'cisx - 3'cisx

transx

3'transx - 5'transx

3'Cisx

Σ#3'cis 3'cisx

3'Transx

Σ#3'trans 3'transx

5'Cisx

Σ#5'cis 5'cisx

5'Transx

Σ#5'trans 5'transx

Cisx

5'Cisx - 3'Cisx

Transx

3'Transx - 5'Transx

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:10.1186/1471-2199-5-10

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