% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR213C.t2k-100-30-dssp-ehl2 Host: farm01 Wed Dec 1 18:53:27 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR213C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.dssps % % 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 YGR213C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR213C.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 318 nodes, 338.61 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(=2.1715) * Reverse)^tau(=0.7553))) % 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 1tlqA 189 -23.86 -10.75 2.19e-01 1fqyA 269 -26.98 -9.63 5.16e-01 1dxrH 258 -20.51 -8.43 1.34e+00 6prcH 258 -20.51 -8.43 1.34e+00 1mjgM 729 -21.65 -8.25 1.55e+00 1oaoC 729 -21.62 -8.23 1.58e+00 1jb0A 755 -29.22 -7.81 2.21e+00 1ih7A 903 -20.29 -7.61 2.60e+00 1p8cA 145 -19.25 -7.52 2.81e+00 1vkeA 133 -19.25 -7.51 2.83e+00 1j4nA 271 -31.61 -7.49 2.88e+00 1g8iA 190 -20.02 -7.40 3.11e+00 1jalA 363 -18.90 -7.15 3.83e+00 1t7rA 269 -19.93 -7.10 3.98e+00 1ks9A 291 -18.59 -7.08 4.05e+00 1i37A 260 -19.82 -7.04 4.21e+00 1rcuA 195 -18.01 -6.76 5.32e+00 1ithA 141 -18.45 -6.72 5.51e+00 1vd5A 377 -20.24 -6.59 6.13e+00 1ru3A 732 -20.21 -6.59 6.13e+00 1aoa 275 -21.32 -6.33 7.66e+00 1dofA 403 -21.01 -6.23 8.38e+00 1t56A 216 -19.34 -6.19 8.70e+00 1tk1A 260 -20.17 -6.17 8.79e+00 1oshA 232 -19.98 -6.11 9.28e+00 1dt6A 473 -19.08 -6.00 1.02e+01 1oa4A 222 -15.30 -5.98 1.04e+01 1vmgA 95 -19.86 -5.95 1.07e+01 4tmkA 213 -16.91 -5.93 1.09e+01 1d2kA 392 -17.99 -5.91 1.10e+01 1dl5A 317 -16.01 -5.86 1.15e+01 1c8oA 300 -15.74 -5.73 1.30e+01 1q5dA 419 -18.18 -5.63 1.42e+01 1iomA 377 -18.64 -5.58 1.48e+01 1gkmA 509 -18.65 -5.54 1.54e+01 1omwA 689 -17.56 -5.52 1.56e+01 1iqpA 327 -16.56 -5.52 1.56e+01 1kwsA 261 -15.32 -5.52 1.56e+01 1fggA 261 -15.32 -5.51 1.57e+01 1fc6A 388 -15.56 -5.49 1.60e+01 1jpzA 473 -20.05 -5.44 1.67e+01 1gtrA 553 -16.17 -5.41 1.72e+01 2sfa 191 -14.66 -5.40 1.74e+01 1f1oA 431 -18.76 -5.37 1.79e+01 1b8fA 509 -18.73 -5.36 1.80e+01 1qtqA 553 -16.05 -5.35 1.83e+01 2eboA 74 -17.56 -5.31 1.88e+01 1clqA 903 -18.04 -5.25 1.99e+01 1ll7A 392 -16.93 -5.24 2.00e+01 1uw4B 248 -21.53 -5.21 2.07e+01 1nrjA 158 -15.90 -5.18 2.12e+01 1itzA 675 -16.66 -5.17 2.14e+01 1n6bA 473 -18.36 -5.16 2.15e+01 1e2xA 243 -18.97 -5.14 2.20e+01 1xy7A 166 -14.05 -5.12 2.24e+01 1v54A 514 -28.68 -5.09 2.29e+01 1eagA 342 -14.26 -5.08 2.33e+01 1n83A 270 -24.07 -5.06 2.36e+01 1wer 334 -20.11 -5.05 2.39e+01 1nyhA 166 -19.00 -5.01 2.48e+01 1q5nA 454 -17.94 -5.01 2.49e+01 1pl5A 142 -19.16 -5.00 2.51e+01 1hw1A 239 -18.89 -4.96 2.58e+01 1e7rA 321 -16.40 -4.94 2.63e+01 5tmpA 213 -15.95 -4.93 2.67e+01 1eysH 259 -17.15 -4.89 2.77e+01 1o63A 219 -14.58 -4.84 2.90e+01 1gfsA 321 -16.39 -4.82 2.96e+01 2hgsA 474 -15.24 -4.81 2.98e+01 1e6uA 321 -16.40 -4.75 3.13e+01 1m0uA 249 -16.71 -4.74 3.18e+01 1bsvA 321 -16.30 -4.73 3.20e+01 1ummA 172 -15.76 -4.64 3.47e+01 1fp1D 372 -16.09 -4.64 3.49e+01 1swxA 209 -19.18 -4.63 3.51e+01 1dbhA 354 -16.96 -4.61 3.58e+01 1bwsA 321 -16.25 -4.60 3.60e+01 2eiaB 206 -16.81 -4.60 3.60e+01 1w6uA 302 -16.67 -4.54 3.84e+01 1s9aA 257 -15.44 -4.53 3.86e+01 1oktA 211 -17.25 -4.52 3.89e+01 1ghpA 258 -15.76 -4.52 3.90e+01 1nr6A 473 -17.82 -4.51 3.94e+01 1jsqA 582 -19.27 -4.49 3.99e+01