% 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. % --------------------------------------------------------------------- % w0.5foo.1.YGR230W.t2k-w0.5.mod Host: cc76 Tue Nov 12 18:13:12 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR230W % --------------------------------------------------------------------- % Inserted Files: YGR230W.t2k-w0.5.mod % Database Files: /projects/compbio/experiments/protein-predict/SAM_T02/data/pdbaa % % 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)) % Single Track Model: YGR230W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 138 nodes, 139.11 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(=3.1195) * Reverse)^tau(=0.7296))) % 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 1fm5A 199 -27.87 -8.83 9.64e-02 1jhwA 347 -26.07 -5.60 2.31e+00 1jxzB 269 -25.72 -5.40 2.84e+00 1nzyA 269 -25.72 -5.31 3.14e+00 1nzyB 269 -25.73 -5.30 3.18e+00 1krcC 567 -26.95 -5.14 3.76e+00 1atiA 505 -27.38 -5.12 3.83e+00 1atiB 505 -27.38 -5.12 3.83e+00 1qs0B 338 -25.39 -4.77 5.62e+00 1kfiA 572 -27.14 -4.68 6.18e+00 7fabL 208 -23.69 -4.63 6.55e+00 1f0zA 66 -21.89 -4.59 6.87e+00 1dt6A 473 -26.77 -4.56 7.10e+00 1kt9A 138 -22.96 -4.56 7.11e+00 1ktgA 138 -22.96 -4.56 7.11e+00 1dfvB 177 -24.05 -4.51 7.49e+00 1adqL 213 -23.38 -4.43 8.19e+00 1nglA 179 -24.07 -4.38 8.67e+00 1dtk 57 -21.63 -4.33 9.11e+00 1k8kE 178 -23.90 -4.24 1.02e+01 1qqsA 174 -23.56 -4.18 1.09e+01 1lilA 212 -23.06 -4.09 1.20e+01 1jmqA 46 -19.82 -3.98 1.36e+01 1ejvC 567 -25.68 -3.89 1.52e+01 1ejuC 567 -25.66 -3.87 1.54e+01 1exzA 141 -23.49 -3.86 1.57e+01 1ejsC 567 -25.65 -3.85 1.58e+01 1qd7H 85 -21.58 -3.85 1.59e+01 1ejtC 567 -25.65 -3.84 1.60e+01 1a32 88 -21.65 -3.84 1.60e+01 1a5mC 566 -25.65 -3.84 1.60e+01 1a5oC 566 -25.65 -3.84 1.60e+01 1fwiC 567 -25.65 -3.83 1.62e+01 1ef2A 566 -25.65 -3.83 1.62e+01 1fwjC 567 -25.65 -3.83 1.63e+01 1a5kC 566 -25.65 -3.83 1.63e+01 1krbC 567 -25.65 -3.83 1.63e+01 1prcC 336 -24.20 -3.82 1.64e+01 1dxrC 336 -24.20 -3.82 1.64e+01 6prcC 336 -24.20 -3.82 1.64e+01 1ejrC 567 -25.65 -3.82 1.64e+01 2kauC 567 -25.65 -3.80 1.68e+01 1k3rA 268 -23.52 -3.65 2.00e+01 1bjmA 216 -22.73 -3.65 2.01e+01 2fb4L 216 -22.65 -3.62 2.08e+01 1a5lC 566 -25.39 -3.59 2.14e+01 1cs1A 386 -24.78 -3.59 2.15e+01 1cs1C 386 -24.78 -3.59 2.15e+01 1ktkE 247 -23.34 -3.58 2.17e+01 1fwcC 567 -25.39 -3.58 2.17e+01 1bftA 101 -21.28 -3.57 2.20e+01 1fwhC 567 -25.33 -3.50 2.40e+01 1kcmA 270 -23.81 -3.48 2.44e+01 1fvzA 271 -23.75 -3.42 2.63e+01 1f98A 125 -21.85 -3.42 2.64e+01 1ioj 57 -20.02 -3.35 2.85e+01 1dszA 86 -20.78 -3.31 3.00e+01 1ecfB 504 -26.21 -3.31 3.01e+01 1ecfA 504 -26.21 -3.31 3.01e+01 1jb3A 131 -21.93 -3.29 3.07e+01 1psrA 100 -21.40 -3.27 3.16e+01 1scfA 273 -24.18 -3.26 3.20e+01 1mcwW 216 -22.94 -3.25 3.22e+01 1a4aA 129 -21.46 -3.22 3.34e+01 2azaA 129 -21.46 -3.22 3.36e+01 8fabA 212 -22.27 -3.20 3.43e+01 1emrA 159 -22.69 -3.19 3.46e+01 1dk1A 86 -20.77 -3.18 3.51e+01 1f7yA 89 -20.83 -3.16 3.58e+01 1kevA 351 -24.03 -3.15 3.64e+01 1pedA 351 -24.03 -3.15 3.64e+01 2mcg1 216 -22.20 -3.14 3.68e+01 1hjdA 101 -21.24 -3.14 3.68e+01 1m2oA 768 -25.73 -3.12 3.78e+01 1tmf3 232 -22.75 -3.10 3.89e+01 1bxnA 485 -24.43 -3.09 3.91e+01 1dclA 216 -22.28 -3.09 3.94e+01