% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 02/04/04_14:53:24 % (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. % --------------------------------------------------------------------- % dsspfoo.1.T0226.t04-100-30-CB_burial_14_7 Host: peep Tue Jul 6 14:17:02 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0226 % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t04.x-seqs,/projects/compbio/experiments/models.97/indexes/t04.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 T0226.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0226.t04.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6593 sequences, 1557114 residues, 291 nodes, 57.17 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 (=10028) sequences: % N / (1 + exp(-(lambda(=1.4182) * Reverse)^tau(=0.7707))) % 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 1c7qA 445 -217.47 -199.48 2.14e-30 1iatA 557 -36.63 -20.63 1.39e-02 1jeoA 180 -28.21 -13.30 6.67e-01 1eziA 228 -24.89 -12.98 7.97e-01 1ct5A 256 -23.32 -10.11 4.17e+00 1vimA 200 -24.63 -9.97 4.52e+00 1bif 469 -23.27 -9.78 5.08e+00 1rypD 241 -20.86 -9.48 6.08e+00 1q16A 1247 -23.00 -9.47 6.12e+00 1fnd 314 -22.30 -9.25 6.96e+00 1zymA 258 -20.81 -9.18 7.27e+00 1fnc 314 -22.25 -9.03 7.98e+00 1j5xA 342 -21.87 -8.44 1.15e+01 1vhqA 232 -19.61 -8.32 1.23e+01 1qh8B 519 -23.38 -8.27 1.27e+01 1hnuA 280 -19.97 -8.24 1.29e+01 1b5tA 275 -22.46 -8.21 1.32e+01 1uocA 289 -22.10 -8.19 1.34e+01 1ryp2 233 -20.03 -8.11 1.41e+01 1qhtA 775 -23.57 -8.02 1.49e+01 1a4iA 301 -19.75 -7.94 1.56e+01 1jk7A 323 -21.46 -7.84 1.66e+01 1l3iA 192 -21.07 -7.81 1.69e+01 1qqfA 277 -18.62 -7.66 1.86e+01 1bt3A 345 -19.29 -7.56 1.99e+01 7odcA 424 -21.54 -7.50 2.06e+01 1q15A 503 -20.79 -7.49 2.08e+01 1ho8A 480 -21.94 -7.47 2.10e+01 1clc 639 -19.81 -7.35 2.27e+01 1fwkA 296 -20.74 -7.33 2.30e+01 1dbtA 239 -18.99 -7.31 2.33e+01 1qj5A 429 -19.17 -7.23 2.44e+01 1eg5A 384 -18.94 -7.20 2.50e+01 1gnd 447 -20.89 -7.11 2.65e+01 1fjmA 330 -20.87 -7.10 2.66e+01 1s72O 116 -17.57 -7.05 2.75e+01 1aop 497 -18.30 -6.99 2.85e+01 1b65A 375 -18.17 -6.99 2.86e+01 1pz1A 333 -19.10 -6.98 2.87e+01 1jy1A 464 -18.52 -6.92 2.98e+01 1h72C 296 -20.37 -6.87 3.09e+01 1l1lA 739 -20.83 -6.87 3.09e+01 1s0aA 429 -18.61 -6.85 3.13e+01 1hyeA 313 -22.33 -6.83 3.17e+01 1t9kA 347 -17.50 -6.82 3.19e+01 1jflA 228 -18.72 -6.75 3.34e+01 1brmA 367 -19.82 -6.74 3.36e+01 1o5hA 214 -18.71 -6.67 3.50e+01 1sxjE 354 -20.43 -6.65 3.56e+01 1rqpA 299 -17.37 -6.60 3.68e+01 1f0jA 377 -18.20 -6.56 3.78e+01 1vhvA 268 -18.86 -6.53 3.84e+01 1moq 368 -21.26 -6.53 3.85e+01 1pjhA 280 -17.85 -6.50 3.92e+01