% 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.YGR038W.t2k-100-30-str Host: cc54 Tue Nov 12 04:31:48 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.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 YGR038W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR038W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 223 nodes, 152.59 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(=2.4274) * Reverse)^tau(=0.7629))) % 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 1dxrM 323 -38.26 -12.02 1.47e-02 6prcM 323 -37.85 -11.72 1.89e-02 2at9 247 -34.94 -11.45 2.37e-02 1is2A 661 -34.76 -10.39 5.88e-02 1m0kA 262 -35.97 -9.02 1.95e-01 1a7m 180 -29.89 -8.93 2.11e-01 153l 185 -28.67 -8.62 2.78e-01 1aw0 72 -25.18 -8.57 2.90e-01 1kgbA 231 -34.73 -7.95 5.10e-01 1c3wA 222 -34.38 -7.73 6.30e-01 1dzlA 505 -30.66 -7.49 7.87e-01 1bgc 174 -28.46 -7.32 9.22e-01 1lki 180 -28.22 -7.28 9.58e-01 1dqeA 137 -28.67 -7.18 1.05e+00 1qaxA 428 -28.52 -7.02 1.22e+00 1fg9C 245 -28.71 -6.81 1.48e+00 1gm0A 142 -26.83 -6.61 1.80e+00 1lghA 56 -26.08 -6.35 2.31e+00 1gbs 185 -25.93 -6.33 2.37e+00 1auk 489 -29.32 -6.18 2.73e+00 1cd9C 175 -28.09 -6.15 2.80e+00 2a3dA 73 -23.12 -6.11 2.93e+00 1k3iA 656 -31.40 -5.88 3.65e+00 1tdj 514 -27.08 -5.79 4.01e+00 1pa2A 306 -27.39 -5.56 5.02e+00 1ycqA 107 -23.95 -5.54 5.14e+00 1ehkA 562 -36.73 -5.52 5.24e+00 1bgeB 175 -26.01 -5.44 5.69e+00 1neu 124 -24.08 -5.38 6.02e+00 2cb5A 453 -27.89 -5.37 6.09e+00 1vib 55 -21.32 -5.32 6.39e+00 1cfr 285 -26.97 -5.28 6.64e+00 1jf9A 408 -26.63 -5.09 8.07e+00 1byb 495 -28.86 -4.95 9.35e+00 2pth 193 -24.44 -4.94 9.39e+00 1mjoA 104 -24.48 -4.88 1.00e+01 1cmcA 104 -24.39 -4.80 1.09e+01 1jbjA 186 -31.04 -4.78 1.11e+01 1cnpA 90 -23.61 -4.75 1.14e+01 1qhvA 195 -26.42 -4.70 1.21e+01 1ekxA 311 -26.19 -4.67 1.24e+01 1l9vA 317 -27.43 -4.64 1.28e+01 1cmaA 104 -24.51 -4.61 1.32e+01 1cmbA 104 -24.24 -4.61 1.32e+01 1knvA 293 -25.93 -4.60 1.34e+01 4crxA 322 -26.36 -4.60 1.34e+01 1jae 471 -28.63 -4.58 1.36e+01 1dkqA 410 -26.64 -4.54 1.42e+01 1kbuA 349 -26.45 -4.54 1.43e+01 1adjA 421 -25.54 -4.53 1.45e+01 1h54B 754 -29.26 -4.52 1.45e+01 3il8 72 -21.97 -4.50 1.48e+01 1gai 472 -31.02 -4.48 1.51e+01 1glm 470 -30.98 -4.46 1.55e+01 3crxA 343 -26.43 -4.41 1.63e+01 1rip 81 -27.91 -4.40 1.66e+01 1a16 440 -28.25 -4.38 1.69e+01 1az9 457 -28.28 -4.34 1.76e+01 1h68A 239 -33.23 -4.32 1.80e+01 1h54A 754 -29.26 -4.32 1.80e+01 1jo5A 48 -22.60 -4.31 1.82e+01 1brd 248 -32.76 -4.30 1.84e+01 1jj2B 337 -29.59 -4.29 1.85e+01 1apxA 249 -28.40 -4.28 1.87e+01 1mngA 203 -24.08 -4.22 2.00e+01 1crxA 322 -25.96 -4.22 2.00e+01 1c0nA 406 -25.67 -4.18 2.09e+01 1dklA 410 -26.80 -4.15 2.15e+01 1ffkB 338 -30.82 -4.10 2.26e+01 1ea3A 164 -23.90 -4.05 2.40e+01 1g8lA 411 -26.26 -4.04 2.41e+01 1fsu 492 -27.87 -4.03 2.46e+01 1b06A 210 -26.57 -3.99 2.54e+01 1ezm 301 -27.94 -3.98 2.59e+01 7atjA 308 -25.37 -3.98 2.59e+01 1qu5A 182 -28.19 -3.96 2.63e+01 1eqfA 280 -24.85 -3.96 2.64e+01 1hy3A 294 -25.05 -3.95 2.65e+01 1hkcA 917 -27.69 -3.94 2.70e+01 1fwyA 331 -24.51 -3.93 2.71e+01 1amx 180 -23.09 -3.90 2.80e+01 1jssA 224 -24.57 -3.90 2.83e+01 2atjA 308 -25.24 -3.87 2.91e+01 1qstA 160 -22.96 -3.84 3.02e+01 2bmhA 455 -27.51 -3.82 3.08e+01 1clh 166 -28.34 -3.82 3.09e+01 1aq6A 253 -23.66 -3.79 3.17e+01 1qhsA 178 -22.35 -3.79 3.18e+01 1d4bA 122 -25.03 -3.77 3.25e+01 2fua 215 -24.40 -3.77 3.26e+01 1qhxA 178 -22.35 -3.76 3.29e+01 1h97A 147 -24.01 -3.74 3.35e+01 1f3mC 297 -24.88 -3.72 3.42e+01 1aa7A 158 -23.62 -3.72 3.44e+01 1f44A 324 -26.10 -3.72 3.44e+01 1aol 228 -26.87 -3.66 3.64e+01 1fsgA 233 -24.12 -3.66 3.68e+01 1qq7A 253 -23.55 -3.63 3.76e+01 1gqpA 221 -23.81 -3.63 3.76e+01 1bu7A 455 -27.29 -3.63 3.77e+01 1ycsA 199 -23.63 -3.63 3.78e+01 1i7gA 287 -26.23 -3.63 3.79e+01 1qb2A 109 -21.28 -3.62 3.81e+01 1bhb 71 -23.58 -3.62 3.84e+01 1dseA 292 -26.95 -3.61 3.86e+01 1e4cP 215 -24.16 -3.58 3.98e+01 1jksA 294 -25.25 -3.58 4.00e+01