% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-T2K, 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, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YDL103C.t2k-100-30-CB_burial_14_7 Host: farm02 Sat Nov 13 02:49:50 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDL1/YDL103C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YDL103C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDL103C.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10735 sequences, 2539893 residues, 478 nodes, 510.46 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 (=10700) sequences: % N / (1 + exp(-(lambda(=1.3368) * Reverse)^tau(=0.8628))) % 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 1vm8A 534 -450.62 -436.67 1.63e-102 1jv1A 505 -444.86 -430.29 3.53e-101 1g97A 459 -47.08 -34.70 1.34e-08 1hm9A 468 -45.53 -32.62 5.56e-08 1hv9A 456 -31.60 -19.13 8.15e-04 1fxjA 331 -30.92 -19.01 8.90e-04 1fwyA 331 -30.10 -18.58 1.22e-03 1tzfA 259 -30.11 -17.46 2.81e-03 1jykA 254 -29.79 -17.11 3.66e-03 1i52A 236 -26.37 -15.72 1.05e-02 1e5kA 201 -25.52 -14.78 2.14e-02 1r4kA 169 -23.96 -11.91 1.99e-01 1qmqA 414 -22.72 -9.99 9.23e-01 1vgwA 231 -20.97 -9.92 9.78e-01 1dz4A 414 -21.58 -9.45 1.43e+00 2cmd 312 -21.18 -9.35 1.55e+00 1phb 414 -21.65 -9.13 1.86e+00 1mp4A 292 -20.30 -9.08 1.94e+00 1si2A 149 -20.55 -8.98 2.09e+00 5cpp 414 -21.11 -8.85 2.33e+00 1fr9A 194 -20.18 -8.75 2.53e+00 1phd 414 -20.80 -8.56 2.98e+00 1cei 94 -23.79 -8.55 3.00e+00 1o1yA 239 -20.94 -8.37 3.46e+00 1unkA 87 -22.42 -8.34 3.54e+00 1h5rA 293 -20.68 -8.30 3.67e+00 1k30A 368 -20.30 -8.23 3.90e+00 1phg 414 -20.45 -8.18 4.05e+00 1mc3A 296 -19.76 -7.90 5.14e+00 1olmA 403 -21.32 -7.87 5.25e+00 1o6uA 403 -21.37 -7.66 6.25e+00 1nf8A 207 -19.67 -7.66 6.27e+00 1g0rA 293 -19.88 -7.62 6.45e+00 1nf9A 207 -19.50 -7.60 6.61e+00 1iuqA 367 -19.99 -7.59 6.65e+00 1ugjA 141 -19.24 -7.58 6.67e+00 1rpxA 230 -18.80 -7.39 7.87e+00 1mldA 314 -19.27 -7.20 9.26e+00 1t3tA 1303 -29.80 -7.17 9.42e+00 1c9fA 90 -17.93 -7.06 1.04e+01 1gdoA 240 -17.26 -7.04 1.06e+01 1ixlA 131 -17.97 -7.00 1.09e+01 1s6yA 450 -21.70 -7.00 1.10e+01 1itwA 741 -21.07 -6.99 1.10e+01 1gdoB 240 -17.02 -6.82 1.27e+01 1lfb 99 -19.80 -6.80 1.30e+01 1tvzA 388 -21.43 -6.79 1.31e+01 1cqqA 180 -19.82 -6.68 1.44e+01 1iugA 352 -17.07 -6.66 1.46e+01 1dvoA 152 -20.34 -6.65 1.48e+01 1qo2A 241 -19.39 -6.64 1.48e+01 1noyA 388 -21.32 -6.64 1.49e+01 1ucpA 91 -18.31 -6.64 1.49e+01 1xffA 240 -16.77 -6.62 1.51e+01 1vicA 262 -20.45 -6.58 1.56e+01 1fxoA 293 -18.92 -6.57 1.57e+01 1ji8A 111 -19.07 -6.55 1.60e+01 1oruA 195 -16.61 -6.54 1.62e+01 1rzrA 332 -18.51 -6.47 1.72e+01 1xl7A 612 -18.16 -6.44 1.76e+01 2gbp 309 -16.13 -6.41 1.80e+01 1qhuA 460 -17.88 -6.41 1.81e+01 1mdbA 539 -17.93 -6.39 1.84e+01 1fsu 492 -17.14 -6.33 1.94e+01 1f60A 458 -20.15 -6.29 2.00e+01 1i6iA 366 -18.06 -6.28 2.02e+01 1konA 249 -17.30 -6.23 2.11e+01 1va6A 518 -18.01 -6.19 2.19e+01 1gca 309 -15.93 -6.09 2.38e+01 2ezh 75 -19.70 -6.05 2.47e+01 1uz5A 402 -26.29 -6.02 2.53e+01 1ig3A 263 -17.26 -5.94 2.70e+01 1v02A 565 -21.06 -5.94 2.70e+01 1qk4A 233 -17.62 -5.92 2.76e+01 1drs 59 -18.31 -5.89 2.82e+01 1gyxA 76 -21.77 -5.89 2.84e+01 1cs1A 386 -16.70 -5.82 3.01e+01 1n3kA 130 -20.46 -5.71 3.31e+01 1dzlA 505 -21.75 -5.67 3.43e+01 1seiA 130 -19.00 -5.65 3.49e+01 1k7kA 221 -16.33 -5.64 3.52e+01 1cs1C 386 -16.61 -5.64 3.52e+01 1ikzA 142 -16.21 -5.60 3.65e+01 1mrg 263 -16.06 -5.59 3.68e+01 1vm6A 228 -16.51 -5.58 3.69e+01 1lvwA 295 -19.09 -5.58 3.72e+01 1rljA 139 -15.73 -5.56 3.76e+01 1u04A 771 -22.29 -5.53 3.88e+01 1iirA 415 -17.42 -5.51 3.93e+01 830cA 168 -16.53 -5.51 3.94e+01 1qgoA 264 -16.63 -5.50 3.97e+01 1odfA 290 -18.06 -5.50 3.97e+01