% 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. % --------------------------------------------------------------------- % strfoo.1.YGR230W.t2k-100-30-str Host: cc76 Tue Nov 12 18:17:10 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.strs % % 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.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 138 nodes, 94.22 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(=1.8184) * Reverse)^tau(=0.8162))) % 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 1dszA 86 -28.28 -10.46 1.14e-01 1nzyA 269 -30.08 -9.18 3.49e-01 1kwmA 402 -30.27 -9.08 3.81e-01 1k3eA 156 -29.22 -8.38 7.14e-01 1ihuA 589 -31.42 -8.13 8.89e-01 1gdtA 183 -28.94 -8.09 9.24e-01 1hra 81 -25.99 -7.90 1.10e+00 1f48A 589 -30.60 -7.31 1.89e+00 3pmgA 561 -30.57 -7.26 1.98e+00 1bza 262 -28.21 -6.41 4.38e+00 1sesA 421 -27.90 -5.80 7.83e+00 1kfiA 572 -28.37 -5.70 8.60e+00 1lxtA 561 -29.44 -5.66 8.99e+00 1pysB 785 -28.83 -5.63 9.23e+00 1cd0A 111 -22.72 -5.52 1.03e+01 1g4wR 383 -27.69 -5.46 1.09e+01 1bsg 266 -26.33 -5.46 1.09e+01 1b7yB 785 -28.52 -5.37 1.19e+01 1iq4A 179 -25.74 -5.26 1.32e+01 1jyoA 130 -25.37 -5.24 1.35e+01 2bpa2 175 -23.94 -5.23 1.36e+01 1hw7A 255 -28.30 -5.22 1.37e+01 1aky 221 -26.77 -5.21 1.38e+01 1kktA 511 -29.17 -5.19 1.41e+01 1iieA 75 -23.77 -5.15 1.47e+01 1ekjA 221 -25.63 -5.07 1.59e+01 2dtr 226 -26.43 -5.07 1.60e+01 1volA 204 -27.10 -5.06 1.60e+01 1bi0 226 -26.34 -5.00 1.70e+01 1erp 38 -20.17 -4.91 1.86e+01 2ay1A 394 -28.31 -4.85 1.98e+01 1g6zA 70 -22.24 -4.84 2.00e+01 2rslA 140 -24.78 -4.80 2.08e+01 1i7fA 292 -27.65 -4.77 2.14e+01 1exbA 332 -26.31 -4.77 2.15e+01 1fslA 143 -25.25 -4.77 2.15e+01 1c4zA 358 -28.18 -4.75 2.19e+01 1binA 143 -25.20 -4.69 2.32e+01 1jksA 294 -26.55 -4.68 2.33e+01 1b0zA 445 -27.57 -4.68 2.35e+01 2pgi 445 -27.57 -4.68 2.35e+01 1tafB 70 -23.56 -4.61 2.52e+01 1gnwA 211 -25.10 -4.59 2.56e+01 1gyfA 62 -21.29 -4.59 2.56e+01 1ekjB 221 -25.48 -4.58 2.58e+01 1b8gA 429 -27.72 -4.58 2.59e+01 1kt9A 138 -23.84 -4.56 2.63e+01 1c7qA 445 -27.46 -4.53 2.72e+01 1ftrA 296 -25.69 -4.48 2.87e+01 1fpqA 372 -26.89 -4.48 2.87e+01 1mhyB 395 -29.40 -4.45 2.96e+01 4pgaA 337 -25.34 -4.42 3.03e+01 1hc7A 477 -26.73 -4.42 3.04e+01 1qrqA 325 -25.88 -4.38 3.15e+01 1g4uS 383 -26.68 -4.37 3.21e+01 1eia 207 -25.88 -4.35 3.27e+01 1d5tA 433 -28.32 -4.34 3.28e+01 1ddnA 226 -26.12 -4.33 3.34e+01 1fwp 139 -23.81 -4.29 3.46e+01 1hr6A 475 -29.68 -4.23 3.67e+01 1a5t 334 -25.96 -4.23 3.67e+01 1dhy 292 -24.07 -4.22 3.72e+01 1bueA 265 -24.59 -4.22 3.73e+01 1hyqA 263 -24.21 -4.21 3.78e+01 1h67A 108 -23.81 -4.17 3.90e+01 1lct 333 -25.36 -4.15 4.00e+01