% 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.YGR035C.t2k-100-30-stride-ebghtl Host: cc41 Fri Nov 8 18:58:55 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR035C % --------------------------------------------------------------------- % 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 YGR035C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR035C.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 117 nodes, 78.52 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(=2.2116) * Reverse)^tau(=0.7383))) % 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 1a3gA 308 -28.47 -8.51 1.18e+00 1l2rA 458 -30.77 -8.15 1.55e+00 1l2qA 458 -30.77 -8.14 1.56e+00 1i1kA 309 -27.89 -7.91 1.87e+00 1c4xA 285 -27.73 -7.54 2.49e+00 1jqgA 433 -28.05 -7.13 3.45e+00 1ggvA 232 -28.18 -7.13 3.45e+00 1c4zA 358 -27.90 -6.86 4.28e+00 1oyb 400 -28.59 -6.73 4.73e+00 1oya 400 -28.59 -6.73 4.75e+00 1qmhA 347 -27.53 -6.69 4.89e+00 7atjA 308 -28.59 -6.61 5.22e+00 1lba 146 -26.62 -6.37 6.32e+00 1oyc 400 -28.11 -6.34 6.50e+00 1gtzA 156 -24.88 -6.24 7.02e+00 1kqfC 217 -27.60 -6.19 7.35e+00 1qasA 622 -29.86 -6.13 7.74e+00 1dhpA 292 -26.41 -6.07 8.09e+00 1qatB 622 -29.73 -6.02 8.43e+00 1bxkA 355 -28.11 -5.96 8.91e+00 1cb0A 283 -28.76 -5.95 8.95e+00 1din 236 -27.98 -5.90 9.37e+00 1djxB 624 -29.53 -5.87 9.54e+00 1djxA 624 -29.52 -5.85 9.75e+00 1l5jA 865 -29.75 -5.81 1.01e+01 1hlrA 907 -28.72 -5.80 1.01e+01 3pmgA 561 -28.62 -5.78 1.03e+01 2atjA 308 -27.58 -5.73 1.08e+01 1d0iA 156 -24.52 -5.69 1.11e+01 1jjiA 311 -26.70 -5.69 1.11e+01 1imjA 210 -26.00 -5.65 1.15e+01 1di0A 158 -24.49 -5.38 1.45e+01 1es6A 296 -25.65 -5.38 1.45e+01 1qe3A 489 -27.83 -5.38 1.45e+01 1jmoA 480 -28.46 -5.37 1.46e+01 1lxtA 561 -28.88 -5.34 1.50e+01 1jy5A 212 -24.86 -5.24 1.63e+01 1ddzA 496 -26.61 -5.20 1.69e+01 1qc5A 192 -25.10 -5.14 1.77e+01 1k4wA 252 -26.05 -5.10 1.84e+01 1e9kA 38 -20.31 -5.08 1.87e+01 1vtp 26 -19.04 -5.03 1.95e+01 1ako 268 -25.21 -5.03 1.96e+01 1xnb 185 -23.14 -5.02 1.97e+01 1d8cA 723 -28.42 -4.87 2.26e+01 1noyA 388 -26.54 -4.85 2.30e+01 1wad 112 -22.34 -4.84 2.31e+01 1bpv 112 -22.13 -4.82 2.35e+01 1g73A 162 -23.17 -4.73 2.54e+01 1ecpA 238 -24.45 -4.69 2.62e+01 1k9sA 237 -24.38 -4.66 2.69e+01 1fj2A 232 -24.59 -4.66 2.71e+01 1de4C 640 -28.42 -4.64 2.76e+01 1k8kD 300 -30.33 -4.63 2.76e+01 1hllA 32 -19.70 -4.63 2.77e+01 3dfr 162 -23.15 -4.62 2.81e+01 2fcr 173 -23.41 -4.58 2.90e+01 1eokA 290 -24.80 -4.56 2.94e+01 1ee4A 423 -26.11 -4.49 3.14e+01 1kbqA 273 -25.32 -4.49 3.15e+01 1bn7A 294 -24.75 -4.46 3.23e+01 1kewA 361 -25.94 -4.45 3.27e+01 1ede 310 -24.57 -4.40 3.40e+01 1pvuA 154 -23.20 -4.37 3.51e+01 1b6g 310 -24.58 -4.36 3.52e+01 1cf2O 337 -24.80 -4.35 3.55e+01 1ax4A 467 -27.39 -4.35 3.56e+01 1sgpI 51 -20.00 -4.34 3.59e+01 4xiaA 393 -26.23 -4.34 3.61e+01 1qrdA 273 -24.22 -4.33 3.64e+01 1qe5A 266 -23.61 -4.32 3.67e+01 1b6sA 355 -25.29 -4.28 3.79e+01 3pviA 157 -22.98 -4.24 3.94e+01