% 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.YEL014C.t2k-100-30-stride-ebghtl Host: cc64 Sat Dec 7 07:04:13 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YEL0/YEL014C % --------------------------------------------------------------------- % 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 YEL014C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL014C.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7458 sequences, 1753770 residues, 102 nodes, 70.22 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(=2.0146) * Reverse)^tau(=0.7621))) % 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 1i7dA 659 -32.64 -11.12 1.66e-01 1eur 365 -30.75 -8.82 9.41e-01 1d6mA 653 -29.49 -8.03 1.73e+00 1e7uA 961 -30.30 -7.24 3.29e+00 1c8oA 300 -28.07 -7.16 3.50e+00 1ky9A 448 -29.35 -6.83 4.59e+00 1qhdA 398 -29.00 -6.79 4.71e+00 1qfxA 460 -29.98 -6.67 5.21e+00 1eut 605 -30.32 -6.65 5.32e+00 1hlcA 129 -27.52 -6.57 5.69e+00 1euu 605 -30.34 -6.56 5.71e+00 1ky9B 448 -28.35 -6.33 6.95e+00 4htcI 65 -24.06 -6.28 7.23e+00 1lxdA 100 -24.43 -5.97 9.37e+00 1h70A 255 -25.83 -5.97 9.41e+00 1e8yA 966 -28.71 -5.78 1.10e+01 1bvqA 141 -25.74 -5.64 1.25e+01 1lo7A 141 -25.21 -5.39 1.55e+01 830cA 168 -24.50 -5.28 1.70e+01 2bpa2 175 -26.58 -5.27 1.71e+01 1h4wA 224 -26.82 -5.17 1.87e+01 1k5jA 124 -25.11 -5.12 1.96e+01 1ixmB 192 -24.08 -5.09 2.01e+01 2bc2A 227 -25.80 -5.07 2.04e+01 1f0cA 305 -27.44 -5.07 2.05e+01 1k24A 253 -29.68 -5.05 2.09e+01 1fhoA 119 -26.21 -5.01 2.15e+01 1cxvA 164 -24.15 -4.89 2.41e+01 2bc2B 227 -25.50 -4.87 2.43e+01 1dpo 223 -26.52 -4.87 2.43e+01 1al0G 175 -25.06 -4.76 2.70e+01 3mddA 385 -25.38 -4.75 2.73e+01 3mdeA 385 -25.38 -4.74 2.75e+01 1tiu 98 -24.14 -4.70 2.85e+01 1xdtR 79 -22.73 -4.64 3.01e+01 1eybA 471 -29.30 -4.61 3.09e+01 1hg8A 349 -27.66 -4.56 3.22e+01 1ey2A 471 -29.20 -4.52 3.34e+01 1e8xA 961 -27.55 -4.51 3.37e+01 1a8p 258 -25.15 -4.51 3.38e+01 4bcl 366 -26.94 -4.51 3.38e+01 1g2iA 166 -23.12 -4.45 3.57e+01 1egdA 396 -24.99 -4.39 3.76e+01 1bwyA 132 -24.92 -4.38 3.80e+01 1fmb 104 -23.37 -4.34 3.94e+01