% 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.YGR219W.t2k-100-30-stride-ebghtl Host: cc60 Tue Nov 12 16:52:44 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR219W % --------------------------------------------------------------------- % 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 YGR219W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR219W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 114 nodes, 77.34 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(=1.8348) * Reverse)^tau(=0.7974))) % 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 1jhfA 202 -29.88 -10.08 2.61e-01 1dkgB 197 -27.78 -8.77 7.63e-01 1pmt 203 -26.98 -7.85 1.67e+00 1dkgA 197 -27.15 -7.71 1.88e+00 1eg3A 261 -26.94 -7.40 2.45e+00 1f3lA 321 -30.74 -7.16 3.00e+00 1jrhI 108 -25.40 -7.11 3.14e+00 1db3A 372 -28.25 -6.87 3.88e+00 1irk 306 -27.56 -6.84 3.97e+00 1kpf 126 -24.33 -6.36 6.06e+00 1bp1 456 -28.89 -6.32 6.30e+00 1edhA 226 -28.62 -6.28 6.51e+00 1ecfA 504 -27.51 -6.25 6.69e+00 1ecfB 504 -27.51 -6.19 7.04e+00 1ewfA 456 -28.54 -6.11 7.61e+00 1ir3A 306 -26.65 -5.93 8.95e+00 1kpeA 126 -23.82 -5.87 9.39e+00 1k4wA 252 -24.87 -5.82 9.84e+00 1rrpB 134 -24.26 -5.79 1.01e+01 2napA 723 -30.32 -5.64 1.17e+01 1cbn 46 -21.03 -5.62 1.18e+01 1cnr 46 -21.03 -5.62 1.18e+01 1ejgA 46 -21.03 -5.62 1.18e+01 1ccm 46 -20.99 -5.53 1.29e+01 1m40A 263 -25.10 -5.49 1.33e+01 1btl 263 -24.96 -5.38 1.48e+01 1c8uA 285 -25.93 -5.37 1.49e+01 1qh4A 380 -26.38 -5.34 1.52e+01 1fqgA 263 -24.96 -5.34 1.52e+01 1blxA 326 -27.21 -5.33 1.54e+01 1dywA 173 -25.16 -5.25 1.65e+01 1fzvA 132 -25.03 -5.24 1.67e+01 1ermA 263 -24.82 -5.16 1.81e+01 1fc2D 224 -25.68 -5.16 1.81e+01 1b63A 333 -25.59 -5.13 1.85e+01 1quqA 129 -23.88 -5.11 1.89e+01 1fg9C 245 -25.46 -5.07 1.96e+01 1auyA 189 -25.29 -5.01 2.06e+01 1m8aA 70 -22.08 -4.94 2.20e+01 1gh7A 419 -27.67 -4.91 2.28e+01 1fyhB 229 -25.75 -4.91 2.28e+01 1k5dB 201 -24.14 -4.85 2.41e+01 1lmq 129 -22.53 -4.76 2.62e+01 1erjA 393 -27.10 -4.75 2.64e+01 1jqhA 308 -25.49 -4.74 2.66e+01 1g0dA 695 -29.40 -4.69 2.80e+01 1qsmA 152 -23.18 -4.61 3.01e+01 1lpuA 332 -25.65 -4.56 3.16e+01 1bmv2 374 -27.15 -4.52 3.28e+01 1i8jA 323 -24.33 -4.51 3.31e+01 1hmr 132 -25.83 -4.51 3.32e+01 1eo1A 124 -24.18 -4.49 3.38e+01 1crn 46 -20.30 -4.46 3.46e+01 1l6sA 323 -24.28 -4.45 3.50e+01 1hms 132 -25.79 -4.45 3.50e+01 1b6e 128 -23.32 -4.39 3.70e+01 1bh5A 183 -24.16 -4.39 3.71e+01 1hmt 132 -25.67 -4.35 3.88e+01