% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (c) 1992-2001 Regents of the University of California, Santa Cruz % % Sequence Alignment and Modeling Software System % http://www.cse.ucsc.edu/research/compbio/sam.html % % ----------------- Citations (SAM, SAM-T2K, HMMs) -------------------- % R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: % Extension and analysis of the basic method, CABIOS 12:95-107, 1996. % K. Karplus, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR014W.t2k-100-30-CB_burial_14_7 Host: farm17.cse.ucsc.edu Sun Mar 19 22:40:52 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR014W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR014W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR014W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 1307 nodes, 2493.12 seconds % % Sequence scores selected if better than: % E-value (Emax 4.0e+01) (select_score=4) % % Simple: NLL-NULL using FIM probabilities % Reverse: NLL-NULL for the reverse sequence NULL model % Calculated when Simple < simple_threshold (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=1.3784) * Reverse)^tau(=0.8134))) % Calculated when Simple < simple_threshold (10000.00) % Rescale E-values or use -dbsize for multiple scoring runs. % Scores sorted by E-value, best first % % Sequence ID Length Simple Reverse E-value X count 1q4gA 553 -34.19 -10.52 1.65e+00 1kx5A 135 -37.80 -10.48 1.70e+00 1dqrA 557 -29.69 -10.48 1.70e+00 1hm5A 558 -29.64 -10.32 1.89e+00 1cqeA 580 -34.19 -10.25 1.98e+00 1u0fA 564 -31.19 -9.68 2.94e+00 1iatA 557 -28.64 -9.50 3.33e+00 1be3D 241 -31.49 -9.33 3.74e+00 1ppjD 241 -32.39 -8.90 5.04e+00 1f8nA 839 -25.25 -8.50 6.72e+00 1ffkJ 164 -31.42 -8.28 7.85e+00 1kjkA 64 -24.39 -8.09 8.95e+00 1ystH 260 -38.73 -7.79 1.11e+01 2bibA 547 -28.46 -7.75 1.15e+01 1b3qA 379 -28.99 -7.71 1.17e+01 1b8eA 162 -21.41 -7.66 1.22e+01 1prcH 259 -36.77 -7.61 1.26e+01 1vqoL 165 -30.96 -7.60 1.28e+01 1f66A 136 -31.55 -7.60 1.28e+01 1z3xA 238 -22.85 -7.53 1.34e+01 1yge 839 -23.52 -7.53 1.34e+01 1fgqA 839 -24.11 -7.44 1.43e+01 1ik6A 369 -19.66 -7.43 1.44e+01 1jj2K 164 -30.46 -7.36 1.52e+01 1s72L 165 -30.59 -7.36 1.52e+01 7taa 478 -19.74 -7.15 1.77e+01 1go3E 187 -24.56 -7.10 1.83e+01 1aoiA 116 -29.69 -7.06 1.90e+01 1vjrA 271 -19.72 -7.04 1.92e+01 6prcH 258 -36.11 -7.04 1.92e+01 1ezvE 185 -31.32 -7.03 1.93e+01 1q16C 225 -28.52 -6.97 2.03e+01 1lnh 857 -26.33 -6.96 2.03e+01 1s7kA 182 -22.17 -6.84 2.21e+01 1dxrH 258 -36.20 -6.79 2.30e+01 1bccD 241 -30.96 -6.79 2.30e+01 1ljrA 244 -19.55 -6.79 2.31e+01 1w8xP 117 -34.88 -6.77 2.34e+01 1rw6A 210 -26.28 -6.75 2.38e+01 1cmkE 350 -27.20 -6.70 2.46e+01 1rovA 857 -25.90 -6.65 2.55e+01 1zd0A 150 -20.86 -6.63 2.59e+01 1jcrA 377 -26.37 -6.59 2.66e+01 1kcmA 270 -25.29 -6.59 2.66e+01 1q42A 201 -25.47 -6.56 2.73e+01 1q8uA 350 -27.79 -6.53 2.79e+01 1zy4A 303 -22.90 -6.53 2.80e+01 1iijA 35 -28.93 -6.51 2.84e+01 1qovH 260 -34.97 -6.50 2.85e+01 1ft1A 377 -25.90 -6.46 2.95e+01 1hwyA 501 -24.71 -6.43 3.01e+01 1q6hA 224 -32.40 -6.40 3.08e+01 1qlaC 256 -27.02 -6.31 3.28e+01 1cdkA 350 -27.49 -6.29 3.33e+01 1apmE 350 -26.87 -6.26 3.42e+01 1d8dA 377 -26.06 -6.25 3.43e+01 1cwvA 492 -24.82 -6.25 3.44e+01 1itkA 731 -21.73 -6.24 3.46e+01 1afoA 40 -24.76 -6.21 3.54e+01 1y5iC 225 -27.61 -6.20 3.57e+01 1g5gB 481 -37.60 -6.19 3.60e+01 1aijH 260 -33.88 -6.16 3.67e+01 1rzhH 260 -33.75 -6.16 3.69e+01 1e19A 314 -19.76 -6.13 3.75e+01 1qexA 288 -31.75 -6.12 3.78e+01 1b35C 282 -37.00 -6.12 3.79e+01 1eqfA 280 -23.04 -6.08 3.92e+01 1d2iA 223 -20.89 -6.08 3.92e+01 1ckv 141 -28.12 -6.07 3.93e+01