% 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. % --------------------------------------------------------------------- % stridefoo.1.YEL010W.t2k-100-30-stride-ebghtl Host: cc70 Mon Nov 11 06:27:17 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YEL0/YEL010W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds % % 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 YEL010W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL010W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 117 nodes, 81.75 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(=1.5297) * Reverse)^tau(=0.8380))) % 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 2hpaA 342 -33.50 -10.50 2.60e-01 1cviA 342 -33.33 -10.48 2.65e-01 1rpa 342 -32.87 -10.19 3.35e-01 1fxoA 293 -29.85 -9.60 5.44e-01 1quqB 121 -27.27 -8.03 2.05e+00 1bet 107 -29.13 -7.98 2.14e+00 1d0nA 729 -30.24 -7.55 3.08e+00 1g0rA 293 -26.88 -6.92 5.35e+00 1a6jA 163 -26.19 -6.86 5.64e+00 1yagG 125 -25.84 -6.77 6.10e+00 1d4xG 126 -25.85 -6.76 6.11e+00 1h5rA 293 -26.50 -6.28 9.41e+00 2pldA 105 -24.75 -6.14 1.06e+01 1a6wL 109 -25.71 -6.08 1.12e+01 1gyxA 76 -23.29 -6.04 1.17e+01 2pleA 105 -23.50 -6.00 1.20e+01 1bncB 449 -27.66 -5.99 1.21e+01 1ah6 220 -26.17 -5.95 1.26e+01 1dv1A 449 -27.64 -5.85 1.37e+01 1lox 662 -29.99 -5.83 1.40e+01 1eg5A 384 -26.71 -5.74 1.51e+01 1a6uL 108 -25.00 -5.74 1.52e+01 12asA 330 -25.73 -5.69 1.58e+01 1bolA 222 -26.46 -5.69 1.59e+01 1ecxA 384 -26.62 -5.64 1.66e+01 1a28A 256 -26.76 -5.40 2.07e+01 1iqaA 160 -25.31 -5.40 2.07e+01 1fj2A 232 -25.57 -5.36 2.14e+01 1k2fA 190 -27.28 -5.33 2.20e+01 1mai 131 -23.40 -5.08 2.77e+01 1xvaA 292 -27.25 -5.00 2.98e+01 1bag 425 -25.94 -4.98 3.02e+01 1dpb 243 -25.12 -4.98 3.04e+01 1prtF 98 -22.99 -4.95 3.11e+01 3lck 271 -25.01 -4.93 3.18e+01 1d2kA 392 -26.67 -4.93 3.19e+01 1f3uB 171 -23.90 -4.90 3.25e+01 1uok 558 -26.62 -4.89 3.29e+01 1hcl 298 -25.02 -4.88 3.32e+01 1irqA 71 -21.97 -4.88 3.33e+01 1g5aA 628 -27.23 -4.80 3.58e+01 1blxA 326 -25.79 -4.79 3.60e+01 1e1xA 299 -24.95 -4.78 3.63e+01 1fiwA 290 -26.39 -4.78 3.65e+01 1bjx 110 -22.95 -4.77 3.69e+01 2bjxA 110 -22.95 -4.77 3.69e+01 1bcpF 99 -22.62 -4.72 3.85e+01 2rslA 140 -23.06 -4.72 3.85e+01 1msc 129 -24.32 -4.71 3.88e+01 1dqaA 467 -26.28 -4.70 3.92e+01 1dqaC 467 -26.28 -4.70 3.92e+01 1bncA 449 -26.45 -4.70 3.94e+01