|
Description of COOP parameters. |
||||
| 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) |
|
| fl |
Frequency of a single nucleotide in each position of the lateral region to be considered specified |
0 – 1 |
≥ 0.6 |
|
| fc |
Frequency of a single nucleotide in each position of the core region to be considered specified |
0 – 1 |
≥ 0.8 |
|
Bortoluzzi et al. BMC Bioinformatics 2005 6:121 doi:10.1186/1471-2105-6-121 |
||||