% 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.YGR038W.t2k-100-30-stride-ebghtl Host: cc54 Tue Nov 12 04:36:57 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR038W % --------------------------------------------------------------------- % 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 YGR038W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR038W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 223 nodes, 150.76 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(=2.5201) * Reverse)^tau(=0.7083))) % 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 1a7m 180 -32.40 -9.95 4.08e-01 1is2A 661 -33.91 -9.48 5.65e-01 1m0kA 262 -35.75 -9.07 7.58e-01 1dseA 292 -33.02 -8.97 8.13e-01 6prcM 323 -36.68 -8.96 8.22e-01 1dxrM 323 -34.93 -8.60 1.07e+00 1lki 180 -29.74 -8.34 1.29e+00 1kgbA 231 -34.78 -8.30 1.33e+00 1bgc 174 -30.02 -8.11 1.53e+00 153l 185 -28.01 -8.03 1.61e+00 1c3wA 222 -34.40 -7.74 2.01e+00 1lghA 56 -26.60 -7.16 3.12e+00 2at9 247 -31.94 -7.11 3.25e+00 1cd9C 175 -29.37 -6.86 3.93e+00 1eqfA 280 -27.61 -6.78 4.20e+00 1bgeB 175 -27.37 -6.39 5.68e+00 1edzA 320 -27.63 -6.29 6.18e+00 1ee9A 320 -27.53 -6.24 6.40e+00 1dzlA 505 -30.39 -6.22 6.51e+00 1gm0A 142 -26.14 -6.22 6.51e+00 1dqeA 137 -28.14 -6.17 6.78e+00 1ryc 294 -29.84 -6.14 6.92e+00 1ehkA 562 -39.56 -6.06 7.42e+00 1aw0 72 -22.36 -5.74 9.61e+00 1ccg 291 -29.58 -5.55 1.13e+01 1gbs 185 -25.22 -5.53 1.14e+01 1bvoA 175 -27.55 -5.40 1.28e+01 1pa2A 306 -27.44 -5.36 1.31e+01 2pth 193 -24.96 -5.33 1.34e+01 1inp 400 -28.93 -5.22 1.47e+01 1gweA 503 -31.31 -5.19 1.51e+01 1ex1A 605 -28.50 -5.16 1.55e+01 1fgyA 127 -24.02 -5.13 1.59e+01 1hbzA 498 -31.43 -5.11 1.62e+01 2a3dA 73 -22.06 -5.10 1.64e+01 1iexA 605 -28.67 -5.07 1.68e+01 1ffkB 338 -30.93 -5.06 1.69e+01 1ffkG 145 -24.53 -5.05 1.70e+01 4lbd 267 -26.75 -5.05 1.71e+01 1vib 55 -20.96 -5.03 1.73e+01 2lbd 267 -26.68 -4.99 1.79e+01 1brd 248 -35.55 -4.98 1.81e+01 1kk1A 410 -27.11 -4.92 1.91e+01 1qaxA 428 -26.30 -4.86 2.00e+01 1a64A 97 -24.21 -4.86 2.00e+01 1uok 558 -29.83 -4.72 2.26e+01 1howA 373 -27.42 -4.70 2.30e+01 7atjA 308 -26.22 -4.66 2.39e+01 1rh2F 165 -26.63 -4.64 2.42e+01 1vcbA 118 -26.01 -4.60 2.51e+01 1auk 489 -28.25 -4.58 2.54e+01 1larA 575 -28.27 -4.58 2.55e+01 1e39A 571 -27.35 -4.58 2.56e+01 1cuk 203 -23.64 -4.57 2.58e+01 1dqzA 280 -25.41 -4.47 2.81e+01 1konA 249 -24.59 -4.46 2.82e+01 1dqyA 283 -25.41 -4.40 3.00e+01 1f5vA 240 -24.25 -4.38 3.04e+01 1fcyA 236 -26.08 -4.29 3.29e+01 2cb5A 453 -26.71 -4.29 3.31e+01 1rypI 222 -26.75 -4.23 3.47e+01 1qjdA 571 -27.36 -4.23 3.48e+01 1bh6A 274 -26.42 -4.22 3.49e+01 1kssA 571 -27.37 -4.20 3.57e+01 1cfr 285 -25.70 -4.19 3.59e+01 1bu8A 452 -27.27 -4.17 3.66e+01 1jj2B 337 -28.34 -4.16 3.69e+01 1neu 124 -23.65 -4.15 3.72e+01 1tdj 514 -25.33 -4.15 3.73e+01 1jbjA 186 -29.58 -4.14 3.77e+01 3lynA 136 -24.51 -4.11 3.86e+01 1ds4A 292 -29.27 -4.11 3.87e+01 1qmqA 414 -27.59 -4.09 3.93e+01