% 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.YGR206W.t2k-w0.5.mod Host: cc57 Tue Nov 12 14:53:50 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR206W % --------------------------------------------------------------------- % Inserted Files: YGR206W.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: YGR206W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 102 nodes, 100.68 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(=2.9947) * Reverse)^tau(=0.7279))) % 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 1hf0A 159 -31.42 -12.63 5.66e-03 1octC 156 -31.04 -12.00 9.40e-03 1cqtA 163 -31.08 -11.99 9.52e-03 1e3oC 160 -28.35 -9.57 7.40e-02 1cydA 244 -28.83 -9.12 1.10e-01 1au7A 146 -26.58 -8.81 1.44e-01 1pou 71 -26.28 -8.29 2.32e-01 1qa9B 95 -22.87 -5.43 3.61e+00 1eepB 404 -25.43 -5.32 4.05e+00 1fvaA 217 -24.44 -5.24 4.40e+00 1k4wA 252 -24.60 -5.09 5.10e+00 1jljA 189 -23.89 -4.99 5.69e+00 1g9pA 45 -20.83 -4.68 7.87e+00 1cczA 171 -23.04 -4.66 8.04e+00 1e3dB 542 -25.77 -4.56 8.97e+00 1hngA 176 -22.94 -4.44 1.01e+01 1fvgA 199 -23.39 -4.44 1.02e+01 1gzsB 165 -22.74 -4.40 1.07e+01 1hcp 76 -21.21 -4.38 1.09e+01 1b8wA 42 -19.69 -4.36 1.11e+01 1hcqA 84 -21.38 -4.35 1.12e+01 1cjbA 231 -24.81 -4.34 1.14e+01 1gl8A 104 -21.79 -4.29 1.19e+01 1fb6A 105 -21.81 -4.28 1.21e+01 1d5yA 292 -25.09 -4.16 1.38e+01 1fpn3 237 -23.15 -4.15 1.39e+01 1jqeA 292 -23.99 -4.11 1.45e+01 1cloL 213 -22.39 -4.10 1.48e+01 1iqcA 308 -23.57 -4.09 1.48e+01 1jqdA 292 -23.99 -4.09 1.49e+01 1m2oB 190 -22.65 -4.07 1.53e+01 1a4yA 460 -25.20 -4.05 1.56e+01 1d0iA 156 -21.94 -3.96 1.73e+01 1aym3 238 -23.06 -3.95 1.73e+01 1gtzA 156 -21.94 -3.95 1.74e+01 1el4A 195 -23.67 -3.90 1.84e+01 1jf2A 195 -23.67 -3.90 1.84e+01 1e6yA 569 -24.46 -3.79 2.08e+01 1dqeA 137 -22.35 -3.78 2.09e+01 1gm0A 142 -22.39 -3.76 2.15e+01 1aifA 215 -21.99 -3.68 2.35e+01 1gya 105 -21.01 -3.66 2.42e+01 1qddA 144 -21.60 -3.63 2.49e+01 1ihcA 188 -22.53 -3.62 2.51e+01 1ab1 46 -19.61 -3.55 2.72e+01 1kw4A 89 -21.30 -3.55 2.74e+01 1dxrL 273 -23.37 -3.53 2.79e+01 1cxrA 46 -19.62 -3.52 2.83e+01 1qa9A 102 -20.94 -3.50 2.90e+01 3sc2B 152 -21.52 -3.48 2.94e+01 1whsB 153 -21.53 -3.48 2.96e+01 1whtB 153 -21.53 -3.48 2.96e+01 1bcsB 160 -21.58 -3.43 3.12e+01 1ygs 234 -22.68 -3.42 3.18e+01 1d9kA 110 -20.67 -3.41 3.19e+01 1lit 144 -21.32 -3.39 3.27e+01 1eupA 403 -24.30 -3.38 3.31e+01 1oxa 403 -24.30 -3.38 3.31e+01 1k7jA 206 -22.44 -3.37 3.35e+01 1bmc 221 -22.38 -3.37 3.35e+01 6prcL 273 -23.20 -3.36 3.38e+01 1bvtA 227 -22.41 -3.36 3.40e+01 1r1a3 238 -22.09 -3.36 3.41e+01 1fqjC 42 -18.17 -3.35 3.44e+01 1g84A 105 -20.35 -3.35 3.45e+01 1e0jB 289 -22.81 -3.34 3.48e+01 1cr1A 296 -22.84 -3.33 3.51e+01 1cr0A 296 -22.84 -3.33 3.51e+01 1fvjA 189 -21.65 -3.31 3.60e+01 1bbg 40 -18.15 -3.30 3.64e+01 3bbg 40 -18.15 -3.30 3.64e+01 1d0sA 356 -23.11 -3.29 3.68e+01 1d0vA 356 -23.11 -3.29 3.68e+01 1jioA 403 -24.30 -3.29 3.69e+01 1jipA 403 -24.30 -3.28 3.71e+01