# gibbs_sampler_ans ../../data/Gibbs/DRB10401.lig # Fri Oct 28 10:58:15 2011 # User: mniel # PWD : /usr/opt/www/pub/CBS/courses/27623.algo/exercises/code/answers # Host: Linux interaction 2.6.16.54-0.2.12-default ia64 # Command line parameters set to: # [-l int] 9 Motif length # [-i int] 50 Number of iterations per train example # [-s int] -1 Seed [-1] Default, [0] Time [>0] Specific seed # [-m filename] -- File for scoring matrix # [-alp string] ARNDCQEGHILKMFPSTWYV Amino acid alphabet # [-pc] 0 Print core of alignment # [-c filename] core File for core # [-ts float] 3.000000 Start temperature # [-te float] 0.000100 Final temperature # [-nt int] 10 Number of temperature steps # [-wlc float] 50.000000 Weigth on low count # [-sw] 0 Include heuristic sequence weighting # [-blf filename] /home/people/mniel/matrices/blosum62.freq_rownorm Real value blosum matrix filename # [-v] 0 Verbose mode # [-noc float] 0.000000 Log-odds score asignment to no count elements # [-p1a] 0 Allow only Hydrophobic AA at P1 # [-p1l filename] ILVMFYW Allowed letters at P1 [Only with -p1a option] # [-factor float] 2.885400 Scale factor for matrix 2/log2 # Read 455 elements on linelist ../../data/Gibbs/DRB10401.lig # Read 455 elements on seqlist ../../data/Gibbs/DRB10401.lig # Number of sequences nseq 455 # Back ground frequences # 0 A 0.07400 # 1 R 0.05200 # 2 N 0.04500 # 3 D 0.05400 # 4 C 0.02500 # 5 Q 0.03400 # 6 E 0.05400 # 7 G 0.07400 # 8 H 0.02600 # 9 I 0.06800 # 10 L 0.09900 # 11 K 0.05800 # 12 M 0.02500 # 13 F 0.04700 # 14 P 0.03900 # 15 S 0.05700 # 16 T 0.05100 # 17 W 0.01300 # 18 Y 0.03200 # 19 V 0.07300 # Read_realblosum done. Alphabet ARNDCQEGHILKMFPSTWYV # Motif length 9. Alen 20 # Number of temperature steps 10 dt 0.299990 # nt Ini T Ini Iteration: Ini Kullbach Leibler distance sum 1.820518 # Iteration: Final Kullbach Leibler distance sum 6.653771 6.653771 Last position-specific scoring matrix computed A R N D C Q E G H I L K M F P S T W Y V 1 A -2.706 -8.577 -5.752 -9.132 -8.795 -6.240 -3.333 -6.734 -3.415 -1.804 0.974 -2.165 -0.581 4.592 4.586 -3.096 -6.523 5.329 3.726 -0.858 2 A -0.478 2.252 -6.152 -2.910 -8.573 -1.058 -2.231 -1.274 -1.389 -1.983 0.328 4.127 -1.617 -2.026 -4.421 0.298 -0.385 -1.076 -2.762 1.498 3 A 1.064 -0.883 1.887 -6.640 -3.462 0.243 -1.310 -1.392 -3.186 -3.595 -1.550 -1.013 -1.273 0.197 -1.546 0.476 -1.695 -2.584 5.655 0.735 4 A 1.657 -6.532 -1.858 2.181 -8.358 0.567 3.223 -3.996 -0.460 0.452 -1.800 -4.414 2.136 -1.342 -8.434 -2.152 -2.650 0.022 -7.800 2.671 5 A 0.793 -1.668 -1.190 -2.346 -8.506 1.411 -4.676 -1.010 -1.389 -0.274 -2.960 3.348 -1.662 1.630 1.459 1.834 -3.631 0.032 -5.648 0.921 6 A -0.203 -1.697 0.136 2.991 -8.650 5.183 -1.283 -0.994 -5.361 -8.160 -2.346 -2.559 -4.211 -6.909 -6.276 0.854 3.645 0.018 -2.373 -2.129 7 A 1.829 -0.084 4.489 -6.225 -0.633 -3.304 -2.315 -0.463 -0.707 -4.023 0.655 -3.573 0.335 -3.726 2.657 -1.674 1.410 -9.039 -2.361 -3.040 8 A 1.750 1.432 -3.915 0.349 0.574 -0.076 -3.063 -7.033 -0.205 -2.732 -1.939 -0.696 -3.359 -2.641 4.334 -0.609 3.674 0.442 -2.342 -5.380 9 A 1.194 -3.393 -7.510 -3.964 -2.723 3.584 -0.948 2.483 -1.396 -3.061 2.144 -0.993 -3.150 -4.759 -8.355 1.893 -0.013 -8.806 -2.807 -2.384 # Log-odds matrix written to file --