# File: C2H2_model_short.dat # May be copied for noncommercial use. # For commercial use, contact Gary Stormo. # # Authors: P.V. Benos, A.S. Lapedes and G.D. Stormo # # Panayiotis V. Benos, Gary D. Stormo # A300 Crabtree Hall, Campus Box 8232, # Dept. Human Genetics, Dept. Genetics, # Graduate School of Public Health, School of Medicine, # University of Pittsburgh, Washington Univ. in St. Louis, # 130 DeSoto Street, 4566 Scott Avenue, # Pittsburgh, PA 15261, U.S.A. St. Louis, MO 63110, U.S.A. # # benos@hgen.pitt.edu stormo@genetics.wustl.edu # # # References # 1. P.V. Benos, A.S. Lapedes and G.D. Stormo, # "Probabilistic code for DNA recognition by proteins of the EGR-family", # J. Mol. Biol., (2002) 323:701-727 # 2. P.V. Benos, A.S. Lapedes, D.S. Fields and G.D. Stormo, # "SAMIE: Statistical Algorithm for Modeling Interaction Energies", # Pac. Symp. Biocomput. (2001) 6:115-126. # # # Last updated: 13.July.2001 # #DESCRIPTION # #This file contains the calculated model for the C2H2 zinc finger protein #family, based on the SAMIE algorithm (Benos et al. (2002) 323:701-727). # SAMIE (NucTotLen) 3 SAMIE (AminTotLen) 3 SAMIE (NucLen) 3 SAMIE (AminLen) 3 SAMIE (UseNuc) 0 1 2 SAMIE (UseAmin) 0 1 2 SAMIE (ContactMatrix) [nt_pos, aa_pos] 2 0 1 1 0 2 // SAMIE (T_matrix) -0.988744 ipos= 0 jpos= 2 ia= 0 jb= 0 3.491163 ipos= 0 jpos= 2 ia= 0 jb= 1 -0.325584 ipos= 0 jpos= 2 ia= 0 jb= 2 3.987259 ipos= 0 jpos= 2 ia= 0 jb= 3 2.652349 ipos= 0 jpos= 2 ia= 1 jb= 0 1.647217 ipos= 0 jpos= 2 ia= 1 jb= 1 4.177341 ipos= 0 jpos= 2 ia= 1 jb= 2 2.172972 ipos= 0 jpos= 2 ia= 1 jb= 3 -0.737846 ipos= 0 jpos= 2 ia= 2 jb= 0 -4.009648 ipos= 0 jpos= 2 ia= 2 jb= 1 -1.576600 ipos= 0 jpos= 2 ia= 2 jb= 2 -2.642248 ipos= 0 jpos= 2 ia= 2 jb= 3 -2.030311 ipos= 0 jpos= 2 ia= 3 jb= 0 -2.697555 ipos= 0 jpos= 2 ia= 3 jb= 1 -2.088369 ipos= 0 jpos= 2 ia= 3 jb= 2 -2.699615 ipos= 0 jpos= 2 ia= 3 jb= 3 2.652349 ipos= 0 jpos= 2 ia= 4 jb= 0 1.647217 ipos= 0 jpos= 2 ia= 4 jb= 1 -0.796516 ipos= 0 jpos= 2 ia= 4 jb= 2 2.172972 ipos= 0 jpos= 2 ia= 4 jb= 3 -0.172102 ipos= 0 jpos= 2 ia= 5 jb= 0 3.840930 ipos= 0 jpos= 2 ia= 5 jb= 1 -0.954965 ipos= 0 jpos= 2 ia= 5 jb= 2 -1.884699 ipos= 0 jpos= 2 ia= 5 jb= 3 -0.639334 ipos= 0 jpos= 2 ia= 6 jb= 0 -1.327427 ipos= 0 jpos= 2 ia= 6 jb= 1 -0.352861 ipos= 0 jpos= 2 ia= 6 jb= 2 -1.534492 ipos= 0 jpos= 2 ia= 6 jb= 3 -0.890796 ipos= 0 jpos= 2 ia= 7 jb= 0 -0.696958 ipos= 0 jpos= 2 ia= 7 jb= 1 -0.946162 ipos= 0 jpos= 2 ia= 7 jb= 2 -0.550198 ipos= 0 jpos= 2 ia= 7 jb= 3 -2.342422 ipos= 0 jpos= 2 ia= 8 jb= 0 -2.769905 ipos= 0 jpos= 2 ia= 8 jb= 1 -2.794514 ipos= 0 jpos= 2 ia= 8 jb= 2 -3.595272 ipos= 0 jpos= 2 ia= 8 jb= 3 -1.572908 ipos= 0 jpos= 2 ia= 9 jb= 0 -2.171645 ipos= 0 jpos= 2 ia= 9 jb= 1 5.705735 ipos= 0 jpos= 2 ia= 9 jb= 2 -2.792314 ipos= 0 jpos= 2 ia= 9 jb= 3 3.663390 ipos= 0 jpos= 2 ia= 10 jb= 0 2.402560 ipos= 0 jpos= 2 ia= 10 jb= 1 4.497214 ipos= 0 jpos= 2 ia= 10 jb= 2 -2.062546 ipos= 0 jpos= 2 ia= 10 jb= 3 -1.926796 ipos= 0 jpos= 2 ia= 11 jb= 0 -1.725871 ipos= 0 jpos= 2 ia= 11 jb= 1 -1.626474 ipos= 0 jpos= 2 ia= 11 jb= 2 -3.354468 ipos= 0 jpos= 2 ia= 11 jb= 3 4.674139 ipos= 0 jpos= 2 ia= 12 jb= 0 3.491163 ipos= 0 jpos= 2 ia= 12 jb= 1 5.333282 ipos= 0 jpos= 2 ia= 12 jb= 2 -1.716209 ipos= 0 jpos= 2 ia= 12 jb= 3 -3.833272 ipos= 0 jpos= 2 ia= 13 jb= 0 3.864291 ipos= 0 jpos= 2 ia= 13 jb= 1 -1.454119 ipos= 0 jpos= 2 ia= 13 jb= 2 -2.727201 ipos= 0 jpos= 2 ia= 13 jb= 3 -1.003519 ipos= 0 jpos= 2 ia= 14 jb= 0 0.928129 ipos= 0 jpos= 2 ia= 14 jb= 1 -3.184561 ipos= 0 jpos= 2 ia= 14 jb= 2 -1.563279 ipos= 0 jpos= 2 ia= 14 jb= 3 -1.119617 ipos= 0 jpos= 2 ia= 15 jb= 0 -0.519139 ipos= 0 jpos= 2 ia= 15 jb= 1 -1.366003 ipos= 0 jpos= 2 ia= 15 jb= 2 -2.544706 ipos= 0 jpos= 2 ia= 15 jb= 3 -1.743317 ipos= 0 jpos= 2 ia= 16 jb= 0 -0.123262 ipos= 0 jpos= 2 ia= 16 jb= 1 -1.455928 ipos= 0 jpos= 2 ia= 16 jb= 2 -2.692962 ipos= 0 jpos= 2 ia= 16 jb= 3 5.006327 ipos= 0 jpos= 2 ia= 17 jb= 0 4.317980 ipos= 0 jpos= 2 ia= 17 jb= 1 -0.536454 ipos= 0 jpos= 2 ia= 17 jb= 2 -0.397727 ipos= 0 jpos= 2 ia= 17 jb= 3 2.652349 ipos= 0 jpos= 2 ia= 18 jb= 0 1.647217 ipos= 0 jpos= 2 ia= 18 jb= 1 4.177341 ipos= 0 jpos= 2 ia= 18 jb= 2 2.172972 ipos= 0 jpos= 2 ia= 18 jb= 3 2.652349 ipos= 0 jpos= 2 ia= 19 jb= 0 1.647217 ipos= 0 jpos= 2 ia= 19 jb= 1 -2.185348 ipos= 0 jpos= 2 ia= 19 jb= 2 2.172972 ipos= 0 jpos= 2 ia= 19 jb= 3 3.565410 ipos= 1 jpos= 1 ia= 0 jb= 0 -1.181931 ipos= 1 jpos= 1 ia= 0 jb= 1 -0.724745 ipos= 1 jpos= 1 ia= 0 jb= 2 -3.827449 ipos= 1 jpos= 1 ia= 0 jb= 3 0.640580 ipos= 1 jpos= 1 ia= 1 jb= 0 -1.515565 ipos= 1 jpos= 1 ia= 1 jb= 1 3.416544 ipos= 1 jpos= 1 ia= 1 jb= 2 -3.254344 ipos= 1 jpos= 1 ia= 1 jb= 3 2.427735 ipos= 1 jpos= 1 ia= 2 jb= 0 -4.004907 ipos= 1 jpos= 1 ia= 2 jb= 1 4.161777 ipos= 1 jpos= 1 ia= 2 jb= 2 3.156593 ipos= 1 jpos= 1 ia= 2 jb= 3 -1.877716 ipos= 1 jpos= 1 ia= 3 jb= 0 -2.616455 ipos= 1 jpos= 1 ia= 3 jb= 1 -1.074887 ipos= 1 jpos= 1 ia= 3 jb= 2 -2.086397 ipos= 1 jpos= 1 ia= 3 jb= 3 0.640580 ipos= 1 jpos= 1 ia= 4 jb= 0 3.568293 ipos= 1 jpos= 1 ia= 4 jb= 1 3.416544 ipos= 1 jpos= 1 ia= 4 jb= 2 2.024827 ipos= 1 jpos= 1 ia= 4 jb= 3 -2.756368 ipos= 1 jpos= 1 ia= 5 jb= 0 -1.834213 ipos= 1 jpos= 1 ia= 5 jb= 1 0.009833 ipos= 1 jpos= 1 ia= 5 jb= 2 -2.740160 ipos= 1 jpos= 1 ia= 5 jb= 3 -2.509550 ipos= 1 jpos= 1 ia= 6 jb= 0 -0.272936 ipos= 1 jpos= 1 ia= 6 jb= 1 -3.241077 ipos= 1 jpos= 1 ia= 6 jb= 2 4.279801 ipos= 1 jpos= 1 ia= 6 jb= 3 2.367239 ipos= 1 jpos= 1 ia= 7 jb= 0 -0.726790 ipos= 1 jpos= 1 ia= 7 jb= 1 4.268432 ipos= 1 jpos= 1 ia= 7 jb= 2 -1.890568 ipos= 1 jpos= 1 ia= 7 jb= 3 2.140460 ipos= 1 jpos= 1 ia= 8 jb= 0 4.162795 ipos= 1 jpos= 1 ia= 8 jb= 1 -0.851725 ipos= 1 jpos= 1 ia= 8 jb= 2 -2.153694 ipos= 1 jpos= 1 ia= 8 jb= 3 3.633538 ipos= 1 jpos= 1 ia= 9 jb= 0 -1.649307 ipos= 1 jpos= 1 ia= 9 jb= 1 5.148262 ipos= 1 jpos= 1 ia= 9 jb= 2 -2.298417 ipos= 1 jpos= 1 ia= 9 jb= 3 1.846719 ipos= 1 jpos= 1 ia= 10 jb= 0 3.941687 ipos= 1 jpos= 1 ia= 10 jb= 1 -1.033363 ipos= 1 jpos= 1 ia= 10 jb= 2 -3.206921 ipos= 1 jpos= 1 ia= 10 jb= 3 -6.365904 ipos= 1 jpos= 1 ia= 11 jb= 0 -2.255145 ipos= 1 jpos= 1 ia= 11 jb= 1 -3.010731 ipos= 1 jpos= 1 ia= 11 jb= 2 -3.957712 ipos= 1 jpos= 1 ia= 11 jb= 3 2.773171 ipos= 1 jpos= 1 ia= 12 jb= 0 4.848245 ipos= 1 jpos= 1 ia= 12 jb= 1 -0.158578 ipos= 1 jpos= 1 ia= 12 jb= 2 -1.460547 ipos= 1 jpos= 1 ia= 12 jb= 3 -3.707923 ipos= 1 jpos= 1 ia= 13 jb= 0 -2.011228 ipos= 1 jpos= 1 ia= 13 jb= 1 -2.240919 ipos= 1 jpos= 1 ia= 13 jb= 2 -2.848830 ipos= 1 jpos= 1 ia= 13 jb= 3 3.157727 ipos= 1 jpos= 1 ia= 14 jb= 0 0.188631 ipos= 1 jpos= 1 ia= 14 jb= 1 -0.448199 ipos= 1 jpos= 1 ia= 14 jb= 2 -1.055082 ipos= 1 jpos= 1 ia= 14 jb= 3 2.807894 ipos= 1 jpos= 1 ia= 15 jb= 0 -2.211160 ipos= 1 jpos= 1 ia= 15 jb= 1 -0.125136 ipos= 1 jpos= 1 ia= 15 jb= 2 -4.241684 ipos= 1 jpos= 1 ia= 15 jb= 3 4.332965 ipos= 1 jpos= 1 ia= 16 jb= 0 -2.878889 ipos= 1 jpos= 1 ia= 16 jb= 1 0.209349 ipos= 1 jpos= 1 ia= 16 jb= 2 -2.574531 ipos= 1 jpos= 1 ia= 16 jb= 3 4.465663 ipos= 1 jpos= 1 ia= 17 jb= 0 -2.550276 ipos= 1 jpos= 1 ia= 17 jb= 1 5.261106 ipos= 1 jpos= 1 ia= 17 jb= 2 -2.467634 ipos= 1 jpos= 1 ia= 17 jb= 3 0.640580 ipos= 1 jpos= 1 ia= 18 jb= 0 3.568293 ipos= 1 jpos= 1 ia= 18 jb= 1 3.416544 ipos= 1 jpos= 1 ia= 18 jb= 2 -3.254344 ipos= 1 jpos= 1 ia= 18 jb= 3 0.640580 ipos= 1 jpos= 1 ia= 19 jb= 0 3.568294 ipos= 1 jpos= 1 ia= 19 jb= 1 -1.565474 ipos= 1 jpos= 1 ia= 19 jb= 2 2.024827 ipos= 1 jpos= 1 ia= 19 jb= 3 -1.970504 ipos= 2 jpos= 0 ia= 0 jb= 0 -0.374775 ipos= 2 jpos= 0 ia= 0 jb= 1 -2.373542 ipos= 2 jpos= 0 ia= 0 jb= 2 -1.778684 ipos= 2 jpos= 0 ia= 0 jb= 3 2.147981 ipos= 2 jpos= 0 ia= 1 jb= 0 2.645507 ipos= 2 jpos= 0 ia= 1 jb= 1 2.431794 ipos= 2 jpos= 0 ia= 1 jb= 2 2.680151 ipos= 2 jpos= 0 ia= 1 jb= 3 -0.695467 ipos= 2 jpos= 0 ia= 2 jb= 0 -1.554876 ipos= 2 jpos= 0 ia= 2 jb= 1 -1.161593 ipos= 2 jpos= 0 ia= 2 jb= 2 -2.199553 ipos= 2 jpos= 0 ia= 2 jb= 3 -1.753058 ipos= 2 jpos= 0 ia= 3 jb= 0 -0.809027 ipos= 2 jpos= 0 ia= 3 jb= 1 -1.093326 ipos= 2 jpos= 0 ia= 3 jb= 2 -1.729276 ipos= 2 jpos= 0 ia= 3 jb= 3 2.147981 ipos= 2 jpos= 0 ia= 4 jb= 0 -2.397506 ipos= 2 jpos= 0 ia= 4 jb= 1 2.431794 ipos= 2 jpos= 0 ia= 4 jb= 2 2.680151 ipos= 2 jpos= 0 ia= 4 jb= 3 0.387235 ipos= 2 jpos= 0 ia= 5 jb= 0 -0.359440 ipos= 2 jpos= 0 ia= 5 jb= 1 0.252606 ipos= 2 jpos= 0 ia= 5 jb= 2 -0.425770 ipos= 2 jpos= 0 ia= 5 jb= 3 3.925717 ipos= 2 jpos= 0 ia= 6 jb= 0 3.667873 ipos= 2 jpos= 0 ia= 6 jb= 1 -1.869776 ipos= 2 jpos= 0 ia= 6 jb= 2 -1.745760 ipos= 2 jpos= 0 ia= 6 jb= 3 -0.870965 ipos= 2 jpos= 0 ia= 7 jb= 0 -1.046820 ipos= 2 jpos= 0 ia= 7 jb= 1 3.378520 ipos= 2 jpos= 0 ia= 7 jb= 2 3.448224 ipos= 2 jpos= 0 ia= 7 jb= 3 -1.498809 ipos= 2 jpos= 0 ia= 8 jb= 0 4.010756 ipos= 2 jpos= 0 ia= 8 jb= 1 -2.441413 ipos= 2 jpos= 0 ia= 8 jb= 2 -3.060248 ipos= 2 jpos= 0 ia= 8 jb= 3 -0.022244 ipos= 2 jpos= 0 ia= 9 jb= 0 -0.839412 ipos= 2 jpos= 0 ia= 9 jb= 1 -1.572282 ipos= 2 jpos= 0 ia= 9 jb= 2 4.617123 ipos= 2 jpos= 0 ia= 9 jb= 3 3.668437 ipos= 2 jpos= 0 ia= 10 jb= 0 3.282007 ipos= 2 jpos= 0 ia= 10 jb= 1 2.914631 ipos= 2 jpos= 0 ia= 10 jb= 2 3.075276 ipos= 2 jpos= 0 ia= 10 jb= 3 -2.383229 ipos= 2 jpos= 0 ia= 11 jb= 0 -1.836026 ipos= 2 jpos= 0 ia= 11 jb= 1 -2.385129 ipos= 2 jpos= 0 ia= 11 jb= 2 4.064767 ipos= 2 jpos= 0 ia= 11 jb= 3 4.609042 ipos= 2 jpos= 0 ia= 12 jb= 0 -0.637336 ipos= 2 jpos= 0 ia= 12 jb= 1 -1.871537 ipos= 2 jpos= 0 ia= 12 jb= 2 -2.153566 ipos= 2 jpos= 0 ia= 12 jb= 3 -1.773681 ipos= 2 jpos= 0 ia= 13 jb= 0 3.667873 ipos= 2 jpos= 0 ia= 13 jb= 1 3.173226 ipos= 2 jpos= 0 ia= 13 jb= 2 3.279034 ipos= 2 jpos= 0 ia= 13 jb= 3 -1.615028 ipos= 2 jpos= 0 ia= 14 jb= 0 -1.979564 ipos= 2 jpos= 0 ia= 14 jb= 1 -5.123773 ipos= 2 jpos= 0 ia= 14 jb= 2 -0.356239 ipos= 2 jpos= 0 ia= 14 jb= 3 -2.555902 ipos= 2 jpos= 0 ia= 15 jb= 0 -2.419281 ipos= 2 jpos= 0 ia= 15 jb= 1 -2.949439 ipos= 2 jpos= 0 ia= 15 jb= 2 -2.923862 ipos= 2 jpos= 0 ia= 15 jb= 3 -2.518790 ipos= 2 jpos= 0 ia= 16 jb= 0 -2.188637 ipos= 2 jpos= 0 ia= 16 jb= 1 -2.692981 ipos= 2 jpos= 0 ia= 16 jb= 2 -2.730090 ipos= 2 jpos= 0 ia= 16 jb= 3 -1.001577 ipos= 2 jpos= 0 ia= 17 jb= 0 -0.742879 ipos= 2 jpos= 0 ia= 17 jb= 1 -1.699844 ipos= 2 jpos= 0 ia= 17 jb= 2 -1.357804 ipos= 2 jpos= 0 ia= 17 jb= 3 2.147981 ipos= 2 jpos= 0 ia= 18 jb= 0 2.645507 ipos= 2 jpos= 0 ia= 18 jb= 1 2.431794 ipos= 2 jpos= 0 ia= 18 jb= 2 -2.375659 ipos= 2 jpos= 0 ia= 18 jb= 3 -2.960877 ipos= 2 jpos= 0 ia= 19 jb= 0 3.060227 ipos= 2 jpos= 0 ia= 19 jb= 1 2.924297 ipos= 2 jpos= 0 ia= 19 jb= 2 3.083252 ipos= 2 jpos= 0 ia= 19 jb= 3