% 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.YGR219W.t2k-100-30-str Host: cc60 Tue Nov 12 16:47:31 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.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 YGR219W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR219W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 114 nodes, 76.95 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(=1.6792) * Reverse)^tau(=0.8170))) % 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 -31.08 -11.39 1.05e-01 1dkgA 197 -30.26 -11.14 1.29e-01 1dkgB 197 -30.03 -10.54 2.09e-01 1pmt 203 -27.47 -8.21 1.44e+00 1irk 306 -29.12 -8.13 1.54e+00 1gh7A 419 -31.14 -7.81 2.03e+00 1ir3A 306 -28.91 -7.77 2.11e+00 1db3A 372 -29.84 -7.74 2.16e+00 1m8aA 70 -24.24 -7.24 3.33e+00 1qh4A 380 -28.13 -7.17 3.54e+00 1kpf 126 -25.51 -7.15 3.58e+00 1kpeA 126 -25.47 -7.12 3.68e+00 1bmv2 374 -29.31 -6.98 4.18e+00 1auyA 189 -27.64 -6.47 6.55e+00 1eg3A 261 -26.38 -6.45 6.63e+00 1g0dA 695 -31.38 -6.25 7.91e+00 1erjA 393 -28.37 -6.20 8.26e+00 1quqA 129 -24.97 -6.03 9.64e+00 1lqtA 456 -27.34 -6.03 9.66e+00 1rrpB 134 -25.27 -6.02 9.77e+00 1jrhI 108 -25.04 -5.90 1.09e+01 1jqhA 308 -26.81 -5.88 1.10e+01 1jwhA 337 -26.23 -5.86 1.12e+01 1mbmA 198 -26.36 -5.83 1.16e+01 1c8uA 285 -26.61 -5.79 1.20e+01 1d2sA 170 -25.62 -5.77 1.22e+01 1kdkA 177 -25.65 -5.73 1.26e+01 1cnuA 137 -26.61 -5.71 1.29e+01 1c0dA 358 -27.68 -5.65 1.36e+01 1btl 263 -25.81 -5.62 1.40e+01 1f5fA 205 -25.85 -5.60 1.42e+01 1ermA 263 -25.80 -5.59 1.44e+01 1cnr 46 -21.05 -5.57 1.47e+01 1jg1A 235 -26.51 -5.56 1.48e+01 1fqgA 263 -25.79 -5.55 1.49e+01 1ewfA 456 -27.90 -5.48 1.59e+01 2napA 723 -28.84 -5.44 1.65e+01 1m40A 263 -25.59 -5.43 1.67e+01 1edhA 226 -29.53 -5.41 1.69e+01 1jyoA 130 -24.21 -5.40 1.71e+01 1bg4 302 -25.51 -5.38 1.73e+01 1fg9C 245 -25.61 -5.36 1.78e+01 1ccm 46 -20.85 -5.35 1.78e+01 1b31A 302 -25.51 -5.31 1.85e+01 1lpuA 332 -26.84 -5.31 1.86e+01 1cbn 46 -20.68 -5.28 1.91e+01 1ejgA 46 -20.68 -5.28 1.91e+01 1hmr 132 -26.97 -5.23 2.00e+01 1k5dB 201 -24.82 -5.19 2.06e+01 1pex 207 -26.15 -5.13 2.18e+01 1tsp 559 -26.94 -5.06 2.34e+01 1lkxA 697 -27.03 -5.05 2.35e+01 1hms 132 -26.76 -5.02 2.42e+01 1fzvA 132 -25.70 -5.02 2.43e+01 1thm 279 -24.55 -4.99 2.48e+01 1fpqA 372 -26.58 -4.98 2.51e+01 1bp1 456 -27.53 -4.97 2.53e+01 1fp1D 372 -26.59 -4.96 2.55e+01 1gzqA 300 -27.60 -4.95 2.58e+01 1hmt 132 -26.66 -4.92 2.65e+01 1tyv 542 -26.92 -4.91 2.68e+01 1rypE 242 -24.84 -4.88 2.75e+01 1tyu 543 -26.82 -4.87 2.78e+01 1qq1A 559 -26.83 -4.84 2.87e+01 1qa1A 554 -26.83 -4.82 2.91e+01 1js8A 394 -26.26 -4.72 3.20e+01 1jn8B 273 -25.28 -4.72 3.20e+01 1jmoA 480 -27.11 -4.69 3.28e+01 1gcqC 70 -21.79 -4.63 3.49e+01 1eceA 358 -26.79 -4.63 3.49e+01 1fgxA 288 -25.29 -4.60 3.59e+01 1kn0A 212 -24.60 -4.56 3.71e+01 1fyhB 229 -25.87 -4.52 3.88e+01 1h7sA 365 -26.62 -4.50 3.94e+01 1k4wA 252 -23.93 -4.49 3.98e+01