https://sourceforge.net/p/estremo/home/Output/Recent changes to OutputenTue, 05 Feb 2013 17:57:35 -0000https://sourceforge.net/p/estremo/home/Output/<div class="markdown_content"><pre>--- v11 +++ v12 @@ -38,6 +38,8 @@ sumGC | Sum of exponentials of energy levels which the recognizer assigns to sites in the background (non-binding sites). sumNCR | Sum of scores assigned to binding sites. TF# | Quantity of transcription factor molecules in organism. + PB Err | The abs of the difference between the TF# and the sum of the probability mass over the genome. + Org ID | A unique hex number that identifies the organism BG | 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. @@ -48,5 +50,3 @@ GC% | The GC% for this NCR. E(n) | Energy level of the n-th position in the NCR. Target | Minimum activation level required for perfect fitness. - PB Err | The abs of the difference between the TF# and the sum of the probability mass over the genome. - Org ID | A unique hex number that identifies the organism </pre> </div>Robert ForderTue, 05 Feb 2013 17:57:35 -0000https://sourceforge.net2f845d7a7b4c5994fcd393c79a9fc851fc5bab8ehttps://sourceforge.net/p/estremo/home/Output/<div class="markdown_content"><pre>--- v10 +++ v11 @@ -1,13 +1,13 @@ 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, R_c, R_f, R_s, MI, gGC, nGC, sumBG, sumNCR, TF#,Bg, Fitness - 297, 4.04, 5.97, 5.12, 7.27, 0.50, 0.50, 1.02e+08, 8.28e+07, 30, 1000, 4.02 +<pre> + Gen, R_c, R_f, R_s, MI, gGC, nGC, sumBG, sumNCR, TF#, PB err, chemPot, beta, + 127, -0.08, 4.97, 0.46, 8.32, 0.50, 0.50, 1.38e+03, 6.97e+01, 10, 3.91e-05, -3.11, 1.66, - Histogram - 0, 9, 10, 10, 11, 15, 4, 10, 11, 7, 16, 14, 12, 26, 40, 55, 750 + Bg, Fitness Max. Fit, Org ID + 1000, 6.39e-04, 1.20e-03, 0x000031CA - Site, p, E(p), Act Targ, GC%, E(1), E(2), ... + Site, p, E(p), Exp Targ, GC%, E(1), E(2), ... TGTAACCG, 0, -15.53, 0.62, 0.50, 0.50, -15.53 TGTTCCCG, 0, -15.90, 0.75, 0.50, 0.62, -15.90 AAGACCAG, 0, -15.88, 0.74, 0.50, 0.50, -15.88 @@ -24,7 +24,7 @@ AATACCAT, 0, -15.41, 0.57, 0.50, 0.25, -15.41 TGGATACT, 0, -15.20, 0.50, 0.50, 0.38, -15.20 TGGAACAC, 0, -15.84, 0.73, 0.50, 0.50, -15.84 - +</pre> <table> <thead> <tr> <th>Field</th> <th>Explanation</th> </tr> </thead> <tbody> <tr> <td>@@ -43,8 +43,10 @@</td> <td></td> </tr> <tr> <td>Site</td> <td>The binding site.</td> </tr> <tr> <td>p</td> <td>The position in the NCR of the best site.</td> </tr> <tr> <td>E(p)</td> <td>The energy level of the best site in this NCR.</td> </tr> <tr> <td>- Act</td> <td>Activation level. How "turned on" the gene associated with this binding site is.</td> </tr> <tr> <td>+ Exp</td> <td>Expression level. How "turned on" the gene associated with this binding site is.</td> </tr> <tr> <td>Targ</td> <td>Minimum activation level to be achieved for perfect fitness</td> </tr> <tr> <td>GC%</td> <td>The GC% for this NCR.</td> </tr> <tr> <td>E(n)</td> <td>Energy level of the n-th position in the NCR.</td> </tr> <tr> <td>Target</td> <td>Minimum activation level required for perfect fitness.</td> </tr> <tr> <td>+ PB Err</td> <td>The abs of the difference between the TF# and the sum of the probability mass over the genome.</td> </tr> <tr> <td>+ Org ID</td> <td>A unique hex number that identifies the organism</td> </tr> <tr> <td></pre></td> <td></td> </tr> </tbody> </table></div>Robert ForderTue, 05 Feb 2013 17:57:00 -0000https://sourceforge.net62d46da9cf594349aaf679039d0e9b1e09540750https://sourceforge.net/p/estremo/home/Output/<pre>--- v9 +++ v10 @@ -1,5 +1,6 @@ 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: +<nowiki> Gen, R_c, R_f, R_s, MI, gGC, nGC, sumBG, sumNCR, TF#,Bg, Fitness 297, 4.04, 5.97, 5.12, 7.27, 0.50, 0.50, 1.02e+08, 8.28e+07, 30, 1000, 4.02 @@ -23,6 +24,7 @@ AATACCAT, 0, -15.41, 0.57, 0.50, 0.25, -15.41 TGGATACT, 0, -15.20, 0.50, 0.50, 0.38, -15.20 TGGAACAC, 0, -15.84, 0.73, 0.50, 0.50, -15.84 +</nowiki> Field | Explanation --------|-------------- </pre>Robert ForderWed, 12 Sep 2012 16:40:16 -0000https://sourceforge.net49f671a08d57661217ab8508b6d586621639ea5chttps://sourceforge.net/p/estremo/home/Output/<pre>--- v8 +++ v9 @@ -1,29 +1,28 @@ 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, R_c, R_f, R_s, MI, gGC, nGC, sumBG, sumNCR, TF#,Bg, Fitness - 297, 4.04, 5.97, 5.12, 7.27, 0.50, 0.50, 1.02e+08, 8.28e+07, 30, 1000, 4.02 + Gen, R_c, R_f, R_s, MI, gGC, nGC, sumBG, sumNCR, TF#,Bg, Fitness + 297, 4.04, 5.97, 5.12, 7.27, 0.50, 0.50, 1.02e+08, 8.28e+07, 30, 1000, 4.02 - Histogram - 0, 9, 10, 10, 11, 15, 4, 10, 11, 7, 16, 14, 12, 26, 40, 55, 750 + Histogram + 0, 9, 10, 10, 11, 15, 4, 10, 11, 7, 16, 14, 12, 26, 40, 55, 750 - Site, p, E(p), Act Targ, GC%, E(1), E(2), ... - TGTAACCG, 0, -15.53, 0.62, 0.50, 0.50, -15.53 - TGTTCCCG, 0, -15.90, 0.75, 0.50, 0.62, -15.90 - AAGACCAG, 0, -15.88, 0.74, 0.50, 0.50, -15.88 - TTCACCAT, 0, -15.82, 0.72, 0.50, 0.38, -15.82 - TGCAACAC, 0, -15.27, 0.52, 0.50, 0.50, -15.27 - TGGTTACG, 0, -15.49, 0.60, 0.50, 0.50, -15.49 - ATGACCAG, 0, -15.86, 0.74, 0.50, 0.50, -15.86 - TGTACGAC, 0, -15.11, 0.47, 0.50, 0.50, -15.11 - ATGTAAGC, 0, -0.85, 0.00, 0.50, 0.38, -0.85 - TACATCAG, 0, -15.26, 0.52, 0.50, 0.38, -15.26 - GGGAACAT, 0, -15.74, 0.69, 0.50, 0.50, -15.74 - AAGTACAG, 0, -15.48, 0.60, 0.50, 0.38, -15.48 - GACCACAA, 0, -0.13, 0.00, 0.50, 0.50, -0.13 - AATACCAT, 0, -15.41, 0.57, 0.50, 0.25, -15.41 - TGGATACT, 0, -15.20, 0.50, 0.50, 0.38, -15.20 - TGGAACAC, 0, -15.84, 0.73, 0.50, 0.50, -15.84 - + Site, p, E(p), Act Targ, GC%, E(1), E(2), ... + TGTAACCG, 0, -15.53, 0.62, 0.50, 0.50, -15.53 + TGTTCCCG, 0, -15.90, 0.75, 0.50, 0.62, -15.90 + AAGACCAG, 0, -15.88, 0.74, 0.50, 0.50, -15.88 + TTCACCAT, 0, -15.82, 0.72, 0.50, 0.38, -15.82 + TGCAACAC, 0, -15.27, 0.52, 0.50, 0.50, -15.27 + TGGTTACG, 0, -15.49, 0.60, 0.50, 0.50, -15.49 + ATGACCAG, 0, -15.86, 0.74, 0.50, 0.50, -15.86 + TGTACGAC, 0, -15.11, 0.47, 0.50, 0.50, -15.11 + ATGTAAGC, 0, -0.85, 0.00, 0.50, 0.38, -0.85 + TACATCAG, 0, -15.26, 0.52, 0.50, 0.38, -15.26 + GGGAACAT, 0, -15.74, 0.69, 0.50, 0.50, -15.74 + AAGTACAG, 0, -15.48, 0.60, 0.50, 0.38, -15.48 + GACCACAA, 0, -0.13, 0.00, 0.50, 0.50, -0.13 + AATACCAT, 0, -15.41, 0.57, 0.50, 0.25, -15.41 + TGGATACT, 0, -15.20, 0.50, 0.50, 0.38, -15.20 + TGGAACAC, 0, -15.84, 0.73, 0.50, 0.50, -15.84 Field | Explanation --------|-------------- </pre>Robert ForderWed, 12 Sep 2012 16:39:46 -0000https://sourceforge.net2dc7843795a9b681ff8b47614a4036c0e1da737chttps://sourceforge.net/p/estremo/home/Output/<pre>--- v7 +++ v8 @@ -1,38 +1,49 @@ 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 + Gen, R_c, R_f, R_s, MI, gGC, nGC, sumBG, sumNCR, TF#,Bg, Fitness + 297, 4.04, 5.97, 5.12, 7.27, 0.50, 0.50, 1.02e+08, 8.28e+07, 30, 1000, 4.02 - 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 + Histogram + 0, 9, 10, 10, 11, 15, 4, 10, 11, 7, 16, 14, 12, 26, 40, 55, 750 + + Site, p, E(p), Act Targ, GC%, E(1), E(2), ... + TGTAACCG, 0, -15.53, 0.62, 0.50, 0.50, -15.53 + TGTTCCCG, 0, -15.90, 0.75, 0.50, 0.62, -15.90 + AAGACCAG, 0, -15.88, 0.74, 0.50, 0.50, -15.88 + TTCACCAT, 0, -15.82, 0.72, 0.50, 0.38, -15.82 + TGCAACAC, 0, -15.27, 0.52, 0.50, 0.50, -15.27 + TGGTTACG, 0, -15.49, 0.60, 0.50, 0.50, -15.49 + ATGACCAG, 0, -15.86, 0.74, 0.50, 0.50, -15.86 + TGTACGAC, 0, -15.11, 0.47, 0.50, 0.50, -15.11 + ATGTAAGC, 0, -0.85, 0.00, 0.50, 0.38, -0.85 + TACATCAG, 0, -15.26, 0.52, 0.50, 0.38, -15.26 + GGGAACAT, 0, -15.74, 0.69, 0.50, 0.50, -15.74 + AAGTACAG, 0, -15.48, 0.60, 0.50, 0.38, -15.48 + GACCACAA, 0, -0.13, 0.00, 0.50, 0.50, -0.13 + AATACCAT, 0, -15.41, 0.57, 0.50, 0.25, -15.41 + TGGATACT, 0, -15.20, 0.50, 0.50, 0.38, -15.20 + TGGAACAC, 0, -15.84, 0.73, 0.50, 0.50, -15.84 - -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. +Field | Explanation +--------|-------------- + Gen. | Number of generations which have elapsed (number of iterations of genetic algorithm). + R_c | Corrected Rsequence (corrects for small sample bias). Rsequence is a measure of the column wise information content in the motif. + R_f | This is the expected value of Rsequence (a measure of the minimum information content required to identify each of the binding sites. + R_s | Rsequence value prioer to correction. + MI | Mutual information. A measure of the dependency between positions in sites. + gGC | Average GC% of all samples taken from the background + nGC | Average GC% of all samples taken from first genomic segments + sumGC | Sum of exponentials of energy levels which the recognizer assigns to sites in the background (non-binding sites). + sumNCR | Sum of scores assigned to binding sites. + TF# | Quantity of transcription factor molecules in organism. + BG | 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. + p | The position in the NCR of the best site. + E(p) | The energy level of the best site in this NCR. + Act | Activation level. How "turned on" the gene associated with this binding site is. + Targ | Minimum activation level to be achieved for perfect fitness + GC% | The GC% for this NCR. + E(n) | Energy level of the n-th position in the NCR. + Target | Minimum activation level required for perfect fitness. </pre>Robert ForderWed, 12 Sep 2012 16:38:57 -0000https://sourceforge.net0a8cca22a0a116840aa9ebad8c8945ca480bba3ahttps://sourceforge.net/p/estremo/home/Output/<pre>--- v6 +++ v7 @@ -3,15 +3,15 @@ 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 + 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 @@ -28,10 +28,11 @@ 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 +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. </pre>Robert ForderTue, 12 Jun 2012 15:35:43 -0000https://sourceforge.net52e50b19c9afd738166eab467a129fa9e01028a8https://sourceforge.net/p/estremo/home/Output/<pre>--- v5 +++ v6 @@ -33,5 +33,5 @@ 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 -Exp. | Expression level. How "turned on" the gene associated with this binding site is. -Target | Minimum expression level required for perfect fitness. +Act. | Activation level. How "turned on" the gene associated with this binding site is. +Target | Minimum activation level required for perfect fitness. </pre>Robert ForderTue, 12 Jun 2012 14:42:12 -0000https://sourceforge.net9d982eaea599ee7288e680a401977c84c8d19442https://sourceforge.net/p/estremo/home/Output/<pre>--- v4 +++ v5 @@ -1,17 +1,17 @@ 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 + 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) Occ(1) Pos(2) Occ(2) Avg.Occ Exp. 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 + 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 @@ -29,9 +29,9 @@ 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. -Occ(1). | Occupancy. How much time the transcription factor spends here. +Score(1). | Score. TF affinity for this position. Pos(2). | The position in the promoter region of the second best site. -Occ(2). | Occupancy. How much time the transcription factor spends here. -Avg.Occ. | The average of the occupancies of all sites in the NCR +Score(2). | Score. TF affinity for this position. +Avg.Score. | The average of the occupancies of all sites in the NCR Exp. | Expression level. How "turned on" the gene associated with this binding site is. Target | Minimum expression level required for perfect fitness. </pre>Robert ForderTue, 12 Jun 2012 14:40:33 -0000https://sourceforge.net6734204693a0478b2dbe0c9a3d407f61e2103684https://sourceforge.net/p/estremo/home/Output/<pre>--- v3 +++ v4 @@ -3,39 +3,35 @@ 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. Occ. Exp. Target - GGGACATG, 0, 0.4857, 1.2688, 1.0000 - AGCGCATC, 0, 0.4972, 1.2988, 1.0000 - CGCAAAGA, 0, 0.4597, 1.2010, 1.0000 - GGAATAGC, 0, 0.4898, 1.2796, 1.0000 - GGAACACG, 0, 0.4983, 1.3019, 1.0000 - GTAACATA, 0, 0.4570, 1.1939, 1.0000 - TGTAAGTG, 0, 0.3969, 1.0369, 1.0000 - TGAACATC, 0, 0.4997, 1.3056, 1.0000 - AGCAAATC, 0, 0.4995, 1.3049, 1.0000 - AGAACGGA, 0, 0.4777, 1.2479, 1.0000 - AGTACACC, 0, 0.4988, 1.3030, 1.0000 - CGTACGGG, 0, 0.4661, 1.2176, 1.0000 - AGTACTTC, 0, 0.4465, 1.1663, 1.0000 - AGGACATA, 0, 0.4609, 1.2041, 1.0000 - GGCCCATG, 0, 0.4204, 1.0982, 1.0000 - CGCATATC, 0, 0.4842, 1.2649, 1.0000 - - + Site Pos(1) Occ(1) Pos(2) Occ(2) Avg.Occ Exp. 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. | The position in the promoter region at which the site is found. -Occ. | Occupancy. How much time the transcription factor spends here. +Pos(1). | The position in the promoter region of the best site. +Occ(1). | Occupancy. How much time the transcription factor spends here. +Pos(2). | The position in the promoter region of the second best site. +Occ(2). | Occupancy. How much time the transcription factor spends here. +Avg.Occ. | The average of the occupancies of all sites in the NCR Exp. | Expression level. How "turned on" the gene associated with this binding site is. Target | Minimum expression level required for perfect fitness. </pre>Robert ForderWed, 18 Jan 2012 19:54:38 -0000https://sourceforge.net22b41e301521a54cc718ded7bb4e2595b4addeb3https://sourceforge.net/p/estremo/home/Output/<pre>--- v2 +++ v3 @@ -1,38 +1,39 @@ -Output is formatted in the following way: - +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. Occ. Exp. Target GGGACATG, 0, 0.4857, 1.2688, 1.0000 AGCGCATC, 0, 0.4972, 1.2988, 1.0000 CGCAAAGA, 0, 0.4597, 1.2010, 1.0000 GGAATAGC, 0, 0.4898, 1.2796, 1.0000 GGAACACG, 0, 0.4983, 1.3019, 1.0000 GTAACATA, 0, 0.4570, 1.1939, 1.0000 TGTAAGTG, 0, 0.3969, 1.0369, 1.0000 TGAACATC, 0, 0.4997, 1.3056, 1.0000 AGCAAATC, 0, 0.4995, 1.3049, 1.0000 AGAACGGA, 0, 0.4777, 1.2479, 1.0000 AGTACACC, 0, 0.4988, 1.3030, 1.0000 CGTACGGG, 0, 0.4661, 1.2176, 1.0000 AGTACTTC, 0, 0.4465, 1.1663, 1.0000 AGGACATA, 0, 0.4609, 1.2041, 1.0000 GGCCCATG, 0, 0.4204, 1.0982, 1.0000 CGCATATC, 0, 0.4842, 1.2649, 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. | The position in the promoter region at which the site is found. Occ. | Occupancy. How much time the transcription factor spends here. </pre>Robert ForderFri, 02 Dec 2011 19:18:22 -0000https://sourceforge.net9652152596de1eac050c454456369b8d185c346e