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       Pos(1) Score(1)   Pos(2)  Score(2)  Avg.Score    Act.    Target
ACGCTACT,  20,    0.4667,    11,     0.4540,   0.2801,      0.0082, 1.0000
CGCCTGCA,  25,    0.4719,    45,     0.4249,   0.2763,      0.0083, 1.0000
ACTTGGCT,  40,    0.4859,    49,     0.4474,   0.2692,      0.0085, 1.0000
AGTCAGCG,  45,    0.4704,    13,     0.4448,   0.2723,      0.0083, 1.0000
AGCTTGAA,  31,    0.4236,    22,     0.4017,   0.2637,      0.0074, 1.0000
AGTTAGGT,  43,    0.4719,     6,     0.4423,   0.2680,      0.0083, 1.0000
CTTTGGCT,  24,    0.4657,     6,     0.4463,   0.2659,      0.0082, 1.0000
CCTCAATT,  39,    0.4194,    49,     0.4166,   0.2730,      0.0074, 1.0000

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.
Pos(1).	The position in the promoter region of the best site.
Score(1).	Score. TF affinity for this position.
Pos(2).	The position in the promoter region of the second best site.
Score(2).	Score. TF affinity for this position.
Avg.Score.	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 required for perfect fitness.