Skip to main content

Table 1 Description of COOP parameters.

From: A multistep bioinformatic approach detects putative regulatory elements in gene promoters

Step

Parameter

Description

Range

Example

Search for pattern occurrences

q

Quorum (minimum number out of N input sequences in which a given pattern must be represented)

1 - N

≥ 20 out of 100 sequences

Clustering

d

Physical distance between 5'-ends of occurrences of patterns of length p

0 - |p|

≤ 2 nucleotides

 

o

Ratio between observed overlapping occurrences of two patterns and their average number of occurrences

0 – 1

≥ 0.8

Consensus building

i

Ratio between the number of nucleotides per alignment position and the total number of lines in the alignment. The maximal number of adjacent positions exceeding the threshold i (m) is further analysed for determining the consensus sequence of the motif

0 – 1

≥ 0.5

 

l

Nucleotide length of the lateral region of the motif

0 - m/2

3 bp (out of 10)

 

f l

Frequency of a single nucleotide in each position of the lateral region to be considered specified

0 – 1

≥ 0.6

 

f c

Frequency of a single nucleotide in each position of the core region to be considered specified

0 – 1

≥ 0.8