% 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.T0196.t04-100-30-CB_burial_14_7 Host: cheep Tue Jun 15 22:12:29 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0196 % --------------------------------------------------------------------- % 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 T0196.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0196.t04.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6473 sequences, 1530840 residues, 117 nodes, 36.75 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 (=9907) sequences: % N / (1 + exp(-(lambda(=2.1449) * Reverse)^tau(=0.7459))) % 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 1jnyA 435 -29.75 -19.00 1.25e-03 1d1nA 99 -23.02 -14.31 2.58e-02 1f60A 458 -21.56 -11.47 1.83e-01 1g7sA 594 -21.38 -10.27 4.34e-01 1d2eA 397 -17.95 -9.15 9.86e-01 1ha3A 405 -18.12 -8.59 1.51e+00 1exmA 405 -17.60 -7.94 2.49e+00 1hdmA 201 -17.17 -7.94 2.50e+00 1fp0A 88 -18.64 -7.28 4.18e+00 1bmqB 88 -16.43 -7.16 4.63e+00 1oe8A 211 -16.18 -6.62 7.12e+00 1qtsA 247 -14.68 -6.09 1.10e+01 1pvmA 184 -15.43 -6.09 1.10e+01 1r0tB 62 -14.79 -5.92 1.27e+01 1kyfA 247 -14.22 -5.69 1.55e+01 1oroA 213 -15.75 -5.66 1.58e+01 1aonO 97 -15.19 -5.64 1.60e+01 1f1gA 154 -13.83 -5.58 1.70e+01 1gpqA 135 -15.13 -5.57 1.71e+01 1iyhA 198 -16.04 -5.56 1.73e+01 1jcv 153 -13.77 -5.54 1.76e+01 1uvqB 198 -14.96 -5.45 1.89e+01 1ryp1 222 -15.26 -5.41 1.96e+01 1cf2O 337 -14.34 -5.34 2.09e+01 1kq6A 141 -15.20 -5.28 2.20e+01 1ae9A 179 -14.08 -5.05 2.68e+01 1el6A 219 -14.47 -5.00 2.79e+01 1ihnA 113 -14.01 -4.89 3.07e+01 1opr 213 -15.55 -4.89 3.09e+01 1qx2A 76 -13.52 -4.85 3.19e+01 1is2A 661 -14.35 -4.84 3.22e+01 1cojA 212 -14.46 -4.79 3.35e+01 1ubkL 534 -12.80 -4.73 3.54e+01 1h2rL 534 -12.89 -4.64 3.83e+01 1yaiA 151 -12.88 -4.59 3.99e+01