% 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. % --------------------------------------------------------------------- % alphafoo.1.YEL014C.t2k-100-30-alpha Host: cc64 Sat Dec 7 07:06:37 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.alphas % % 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.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7458 sequences, 1753770 residues, 102 nodes, 69.73 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(=3.0289) * Reverse)^tau(=0.7262))) % 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 1ky9B 448 -29.12 -8.20 2.44e-01 1ky9A 448 -29.33 -7.90 3.23e-01 830cA 168 -26.31 -7.81 3.49e-01 1cxvA 164 -25.77 -7.31 5.55e-01 1c8oA 300 -27.25 -7.31 5.58e-01 1eur 365 -27.17 -6.73 9.70e-01 1f0cA 305 -26.26 -6.17 1.68e+00 1i7dA 659 -27.25 -6.06 1.86e+00 1hlcA 129 -25.62 -6.06 1.87e+00 1d6mA 653 -27.13 -5.98 2.02e+00 4htcI 65 -22.31 -5.82 2.37e+00 1qfxA 460 -28.19 -5.72 2.61e+00 1eybA 471 -27.92 -5.64 2.84e+00 1ey2A 471 -27.94 -5.61 2.93e+00 1h4wA 224 -25.48 -5.60 2.96e+00 1eut 605 -28.00 -5.14 4.71e+00 1tiu 98 -23.27 -5.03 5.32e+00 1euu 605 -28.00 -5.00 5.50e+00 1dst 228 -24.53 -4.98 5.57e+00 1tit 98 -22.92 -4.94 5.83e+00 1dazC 99 -23.14 -4.90 6.06e+00 2bc2A 227 -24.44 -4.84 6.46e+00 2bc2B 227 -24.29 -4.83 6.57e+00 4sgbI 51 -20.46 -4.75 7.12e+00 1qhuA 460 -26.57 -4.74 7.21e+00 1k1tA 99 -22.97 -4.71 7.44e+00 4bcl 366 -25.59 -4.68 7.67e+00 1kzkA 99 -22.73 -4.68 7.67e+00 1ejfA 125 -23.69 -4.64 8.00e+00 1ei5A 520 -26.46 -4.63 8.08e+00 1fa8A 135 -22.70 -4.60 8.32e+00 1eaxA 241 -24.31 -4.57 8.62e+00 1ee6A 197 -23.55 -4.51 9.20e+00 1hy7A 173 -22.75 -4.51 9.22e+00 1iicA 422 -25.26 -4.47 9.64e+00 1ewfA 456 -25.21 -4.41 1.03e+01 1h8pA 109 -24.06 -4.37 1.07e+01 1a7s 221 -23.94 -4.33 1.12e+01 1k92A 455 -24.40 -4.33 1.12e+01 1e6fA 143 -23.05 -4.32 1.13e+01 1f9zA 135 -22.38 -4.30 1.16e+01 1bec 238 -24.25 -4.18 1.32e+01 1lci 550 -26.13 -4.09 1.45e+01 1agx 331 -23.31 -4.09 1.45e+01 1hfs 160 -22.33 -4.02 1.57e+01 2eifA 136 -23.07 -4.01 1.58e+01 1bwyA 132 -22.48 -3.98 1.64e+01 1hvc 203 -23.47 -3.96 1.69e+01 1lvl 458 -24.05 -3.91 1.77e+01 1k24A 253 -25.71 -3.89 1.81e+01 1ha1 184 -22.16 -3.88 1.83e+01 1dnlA 199 -22.78 -3.86 1.87e+01 1h70A 255 -22.79 -3.85 1.90e+01 1g79A 218 -23.00 -3.84 1.92e+01 1difA 99 -21.53 -3.82 1.97e+01 1ndoA 449 -24.56 -3.79 2.02e+01 1bv8A 138 -22.07 -3.78 2.04e+01 1ao8 162 -21.94 -3.76 2.10e+01 1tap 60 -20.12 -3.76 2.11e+01 1dpo 223 -23.32 -3.74 2.14e+01 1bp1 456 -24.47 -3.73 2.16e+01 1ixmB 192 -21.98 -3.73 2.16e+01 1mc0A 368 -23.94 -3.72 2.20e+01 1mpyA 307 -24.26 -3.71 2.21e+01 1prs 173 -22.44 -3.68 2.29e+01 1e7uA 961 -26.08 -3.68 2.31e+01 1gp0A 143 -22.59 -3.67 2.32e+01 1jrrA 382 -25.32 -3.66 2.34e+01 1hg8A 349 -24.18 -3.64 2.41e+01 1eg9A 449 -24.54 -3.63 2.43e+01 1bio 228 -23.67 -3.58 2.57e+01 1bxxA 285 -25.13 -3.56 2.63e+01 1jevA 517 -24.02 -3.51 2.79e+01 1d0dA 60 -19.59 -3.49 2.84e+01 2olbA 517 -24.02 -3.48 2.90e+01 1l3kA 196 -21.95 -3.47 2.91e+01 1prr 173 -22.13 -3.44 3.01e+01 1gky 187 -22.09 -3.43 3.05e+01 1m7bA 184 -21.80 -3.41 3.14e+01 1k0eA 453 -26.54 -3.40 3.17e+01 1iyaA 187 -22.00 -3.39 3.21e+01 1cqyA 99 -21.68 -3.36 3.30e+01 1bw8A 321 -25.22 -3.36 3.32e+01 1i31A 314 -25.08 -3.34 3.38e+01 1bak 119 -20.80 -3.34 3.39e+01 1qsvA 101 -21.61 -3.34 3.40e+01 1j8rA 196 -24.27 -3.33 3.42e+01 1ex7A 186 -21.96 -3.33 3.42e+01 1dbqA 289 -23.18 -3.26 3.71e+01 1k4nA 192 -22.59 -3.25 3.78e+01 1hj9A 226 -23.72 -3.24 3.83e+01 1kigI 60 -19.55 -3.23 3.85e+01 1fmb 104 -21.24 -3.23 3.86e+01 5hvpA 99 -21.19 -3.22 3.91e+01