ScanWM-PL

Input
Sequences   File with fasta sequences. In the current version of program, the maximal number of symbols in a line of FASTA file = 999.
Output
Result   Name of the output file
Options
Threshold typethreshold type, formula to calculate weight matrix cut-off value:

Based on weights of training motifs - formula is:
Cut-off = Average + THR_VALUE * Std_dev
"Average" and "Std_dev" (standard deviation) are calculated for weights of motifs from which a weight matrix has been built. THR_VALUE is a real number (including 0). THR_VALUE is specified by "Threshold value" option.

Based on similarity to weight matrix - formula is:
Cut-off = WM_Min_Value + THR_VALUE * (WM_Max_Value - WM_Min_Value)
"WM_Min_Value" and "WM_Max_Value" are minimal and maximal values that can be obtained with a corresponding weight matrix. THR_VALUE must belong to interval [0;1] (with default value = 0.9). THR_VALUE is specified by "Threshold value" option.
Threshold valuethreshold value
DNA chainDNA chain:
Direct
Reverse
Both