Output

A brief description of the output format for ESTReMo. Each generation, statistics on the fittest organism in the population are written to the output file. They have the following form:

Gen.  Adj. Rseq  Rfreq     Rseq      MI        BG-Sum    NCR-Sum   TFs        BG-Size    Fitness
772,  5.046941,  5.965784, 6.128962, 5.047216, 4.476329, 7.538286, 34.000000, 1000,      0.000000

Site       SitePos SiteScore  AvgScore   Act.    Target  Score(1) Score(2) ...
ACGCTACT,  20,     0.4667,    0.2801,    0.0082, 1.0000, 0.4667,  0.1332
CGCCTGCA,  25,     0.4719,    0.2763,    0.0083, 1.0000, 0.0021,  0.4719
ACTTGGCT,  40,     0.4859,    0.2692,    0.0085, 1.0000, 0.1332,  0.4859
AGTCAGCG,  45,     0.4704,    0.2723,    0.0083, 1.0000, 0.4704,  0.1231
AGCTTGAA,  31,     0.4236,    0.2637,    0.0074, 1.0000, 0.4236,  0.0001
AGTTAGGT,  43,     0.4719,    0.2680,    0.0083, 1.0000, 0.4719,  0.0022
CTTTGGCT,  24,     0.4657,    0.2659,    0.0082, 1.0000, 0.1192,  0.4657
CCTCAATT,  39,     0.4194,    0.2730,    0.0074, 1.0000, 0.3321,  0.4194

Field	Explanation
Gen.	Number of generations which have elapsed (number of iterations of genetic algorithm).
Adj. Rseq	Corrected Rsequence (corrects for small sample bias). Rsequence is a measure of the column wise information content in the motif.
Rfreq	This is the expected value of Rsequence (a measure of the minimum information content required to identify each of the binding sites.
Rseq	Rsequence value prioer to correction.
MI	Mutual information. A measure of the dependency between positions in sites.
BG-Sum	Sum of scores which the recognizer assigns to sites in the background (non-binding sites).
NCR-Sum	Sum of scores assigned to binding sites.
TFs	Quantity of transcription factor molecules in organism.
BG-Size	Number of times the background is sampled (analgous to the size of the genome).
Fitness	How fit is the organism (lower is better, zero is perfect).
Site	The binding site.
SitePos	The position in the promoter region of the best site.
SiteScore	TF affinity for the best site in this NCR.
AvgScore.	The average of the occupancies of all sites in the NCR
Act.	Activation level. How "turned on" the gene associated with this binding site is.
Target	Minimum activation level to be achieved for perfect fitness
Score(n).	Score. TF affinity for the n-th position in the NCR.

Target | Minimum activation level required for perfect fitness.