Table 1 Definition of terms used in describing the algorithms presented in Methods.
Symbol | Meaning |
|---|---|
Σ | alphabet (usually DNA or IUPAC) |
f | input sequences |
f i | i-th input sequence |
f ij | j-th position of the i-th input sequence |
N | number of input sequences |
n i | length of f i |
k | motif size |
S p | p-th prior (in PSP format) |
â„“ | number of priors (it can be zero) |
S | S = 〈S1, ..., Sℓ〉 is the list of all priors |
z min | minimum number of motifs expected to be returned by a RISOTTO run |
z max | maximum number of motifs expected to be returned by a RISOTTO run |
z | number of top motifs post-processed from RISOTTO output |
| the set with the z top motifs to be post-processed by GRISOTTO |
m | motif of size k |
m〈i, α〉 | motif m where the i-th position (starting with 0) is replaced by α ∈ Σ |
ε | empty motif (its BIS score is the minimum possible value) |
f i [j ... j + k - 1] | k-long segment of the i-th input sequence that starts at position j |
S p [i, j] | prior probability at the j-th position of f i |
j i | annotated position for f i with maximum BIS score for a motif m |
P m | probability distribution given by the PSSM induced by m |
α p | the weight of the p-th prior |
λ | coefficient to balance priors and over-representation contribution |
