% 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.YGR030C.t2k-100-30-str Host: cc50 Fri Nov 8 18:31:30 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR030C % --------------------------------------------------------------------- % 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 YGR030C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR030C.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 159 nodes, 107.03 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(=1.5238) * Reverse)^tau(=0.7867))) % 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 1mldA 314 -35.51 -11.68 4.81e-01 1qfrA 89 -29.39 -10.15 1.32e+00 1preB 470 -31.87 -9.73 1.75e+00 1preA 470 -31.11 -8.85 3.18e+00 1mdl 359 -30.16 -8.64 3.68e+00 2mnr 357 -29.98 -8.56 3.89e+00 1ptf 88 -27.64 -8.55 3.90e+00 1a26 361 -29.74 -8.39 4.37e+00 1fp2A 352 -30.73 -8.08 5.42e+00 1ig8A 486 -33.19 -8.05 5.54e+00 1efyA 350 -29.35 -8.05 5.54e+00 1fpxA 352 -30.65 -8.03 5.60e+00 1jqeA 292 -31.05 -7.55 7.90e+00 1hy3A 294 -28.16 -7.42 8.66e+00 1k7hA 476 -29.22 -7.38 8.90e+00 1a4mA 349 -29.82 -6.86 1.29e+01 1dt9A 437 -29.79 -6.74 1.41e+01 1lu9A 287 -28.58 -6.73 1.42e+01 1fkx 349 -29.72 -6.65 1.51e+01 1gk8A 475 -29.15 -6.64 1.52e+01 1hqkA 154 -28.53 -6.59 1.58e+01 1h0xA 100 -28.78 -6.58 1.59e+01 1j5yA 187 -27.14 -6.53 1.65e+01 1knvA 293 -28.77 -6.51 1.67e+01 1a79A 171 -26.40 -6.50 1.68e+01 1add 349 -29.30 -6.48 1.71e+01 1e4fT 419 -28.76 -6.48 1.71e+01 1tubA 440 -29.73 -6.46 1.73e+01 1eudB 396 -29.52 -6.42 1.78e+01 1bn6A 294 -27.91 -6.40 1.80e+01 1cqwA 295 -27.81 -6.40 1.82e+01 1bn7A 294 -27.79 -6.35 1.87e+01 1e19A 314 -28.98 -6.32 1.92e+01 1nsf 273 -29.87 -6.32 1.92e+01 1eo6A 117 -26.89 -6.29 1.96e+01 1cznA 169 -28.22 -6.23 2.05e+01 1eucB 396 -29.26 -6.22 2.06e+01 1ig3A 263 -28.79 -6.19 2.10e+01 1ofv 169 -28.12 -6.13 2.20e+01 1jffA 451 -30.68 -6.08 2.29e+01 1ig0A 319 -27.48 -6.07 2.31e+01 1thg 544 -29.18 -6.06 2.32e+01 8rucA 475 -28.35 -6.03 2.38e+01 1dxrL 273 -26.89 -6.03 2.39e+01 1amuA 563 -28.53 -6.01 2.42e+01 1a7aA 432 -27.55 -6.00 2.44e+01 6prcL 273 -26.88 -5.99 2.46e+01 1dkuA 317 -28.73 -5.92 2.59e+01 1jkmA 358 -28.22 -5.86 2.71e+01 1hstA 90 -23.98 -5.85 2.72e+01 1gw0A 559 -28.17 -5.80 2.82e+01 1fvgA 199 -25.50 -5.80 2.83e+01 1fvaA 217 -25.64 -5.79 2.84e+01 1i19A 561 -29.33 -5.73 2.98e+01 1dszB 85 -23.50 -5.71 3.02e+01 1k55A 246 -26.53 -5.65 3.17e+01 1lk3A 160 -25.42 -5.64 3.19e+01 1ihmA 530 -27.89 -5.64 3.19e+01 1gt7A 274 -25.95 -5.60 3.29e+01 1fviA 297 -27.53 -5.57 3.35e+01 1gr8A 412 -26.59 -5.54 3.43e+01 1ggvA 232 -27.50 -5.54 3.44e+01 1qfoC 119 -23.53 -5.47 3.62e+01 3chbD 104 -23.98 -5.45 3.69e+01 1jkmB 361 -28.36 -5.42 3.75e+01 1kllA 130 -24.77 -5.41 3.79e+01 1k4fA 248 -26.27 -5.40 3.83e+01 1d2nA 272 -28.81 -5.39 3.86e+01 1e3uA 246 -26.25 -5.39 3.86e+01