% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR230W.t2k-100-30-dssp-ehl2 Host: cc76 Tue Nov 12 18:29:55 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR230W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.dssps % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR230W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR230W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 138 nodes, 93.79 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 (0.00) % E-value on N (=7316) sequences: % N / (1 + exp(-(lambda(=1.8750) * Reverse)^tau(=0.8181))) % Calculated when Simple < simple_threshold (0.00) % 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 1ihuA 589 -34.28 -10.68 6.63e-02 1f48A 589 -33.61 -10.00 1.22e-01 1nzyA 269 -29.92 -8.96 3.15e-01 1dszA 86 -27.08 -8.74 3.85e-01 1gw5B 591 -33.56 -7.02 1.93e+00 1fntc 245 -28.76 -6.92 2.13e+00 1hra 81 -25.48 -6.91 2.16e+00 1bza 262 -27.00 -6.61 2.86e+00 1hyqA 263 -27.13 -6.51 3.18e+00 3minC 491 -29.05 -6.38 3.58e+00 1gdtA 183 -26.94 -6.26 4.04e+00 1fwcC 567 -28.21 -6.02 5.10e+00 2minA 491 -28.42 -5.71 6.96e+00 1jksA 294 -27.08 -5.67 7.24e+00 1kfiA 572 -28.49 -5.61 7.71e+00 1kwmA 402 -26.85 -5.58 7.93e+00 1k3eA 156 -25.68 -5.55 8.18e+00 1g6zA 70 -22.32 -5.52 8.42e+00 3pmgA 561 -30.42 -5.41 9.41e+00 1jli 112 -26.26 -5.32 1.02e+01 1pkn 530 -28.03 -5.28 1.07e+01 1k8kE 178 -25.99 -5.20 1.16e+01 1pmi 440 -28.34 -5.15 1.22e+01 1ef8A 261 -27.32 -5.12 1.27e+01 1aky 221 -27.00 -5.03 1.38e+01 1kt9A 138 -23.53 -5.01 1.40e+01 2rslA 140 -25.26 -4.95 1.50e+01 2fsp 124 -24.78 -4.92 1.54e+01 1binA 143 -25.25 -4.91 1.57e+01 1kktA 511 -28.97 -4.86 1.64e+01 4pgaA 337 -26.23 -4.79 1.77e+01 1lct 333 -26.38 -4.79 1.77e+01 1a8y 367 -27.54 -4.76 1.81e+01 1isaA 192 -24.72 -4.73 1.87e+01 1iscA 192 -24.72 -4.73 1.88e+01 1g4wR 383 -27.14 -4.71 1.92e+01 1fslA 143 -25.10 -4.69 1.95e+01 1erp 38 -20.31 -4.68 1.98e+01 1h67A 108 -24.31 -4.66 2.01e+01 1hx0A 496 -26.56 -4.62 2.10e+01 1gyfA 62 -21.12 -4.55 2.25e+01 1iieA 75 -23.13 -4.55 2.26e+01 1ep3A 311 -27.56 -4.47 2.44e+01 1psrA 100 -24.52 -4.47 2.45e+01 1lxtA 561 -29.96 -4.47 2.46e+01 1vid 221 -25.55 -4.47 2.47e+01 1gnwA 211 -24.97 -4.46 2.47e+01 1fy2A 229 -24.72 -4.46 2.49e+01 1h6pA 203 -26.48 -4.44 2.53e+01 1fbaA 361 -26.03 -4.44 2.54e+01 2aaa 484 -26.03 -4.42 2.57e+01 1a32 88 -24.31 -4.40 2.63e+01 1a49A 530 -27.33 -4.33 2.84e+01 1hstA 90 -23.90 -4.27 3.02e+01 1crzA 403 -24.55 -4.26 3.05e+01 1a5t 334 -26.06 -4.21 3.21e+01 1csh 435 -26.81 -4.17 3.35e+01 1amz 435 -26.81 -4.15 3.44e+01 1g5pA 289 -24.55 -4.07 3.73e+01 1ez1A 392 -25.22 -4.06 3.78e+01 1ewkA 490 -26.68 -4.06 3.78e+01 1rom 403 -26.96 -4.05 3.82e+01 1eyzA 392 -25.17 -4.04 3.83e+01 1hmcA 148 -25.00 -4.03 3.89e+01 1k8kG 151 -24.82 -4.02 3.92e+01 1fp6A 289 -24.50 -4.01 3.97e+01