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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