% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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.YGR236C.t2k-100-30-dssp-ehl2 Host: farm16.cse.ucsc.edu Fri Mar 3 09:01:27 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR236C % --------------------------------------------------------------------- % 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 YGR236C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR236C.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14381 sequences, 3373755 residues, 96 nodes, 159.68 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 (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=2.7486) * Reverse)^tau(=0.7174))) % Calculated when Simple < simple_threshold (10000.00) % 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 1zvdA 380 -16.62 -8.04 1.10e+00 1r12A 258 -15.69 -7.11 2.38e+00 1yaxA 153 -15.03 -6.98 2.67e+00 1nt4A 391 -15.97 -6.76 3.22e+00 1lbeA 258 -15.61 -6.73 3.31e+00 1x9mA 698 -15.75 -6.23 5.09e+00 1eni 138 -14.62 -5.95 6.57e+00 1urqA 63 -14.80 -5.90 6.87e+00 1enk 138 -14.62 -5.85 7.17e+00 1exbA 332 -14.48 -5.61 8.92e+00 1vasA 137 -14.53 -5.61 8.93e+00 1zsxA 347 -14.54 -5.57 9.20e+00 1s5lX 50 -15.60 -5.54 9.47e+00 1enj 138 -14.27 -5.52 9.67e+00 1h6hA 143 -13.60 -5.51 9.75e+00 1xc0A 33 -13.14 -5.49 9.94e+00 2end 138 -14.08 -5.48 1.00e+01 1sgg 75 -13.63 -5.40 1.08e+01 1t7pA 698 -14.83 -5.35 1.13e+01 1z83A 196 -13.96 -5.32 1.16e+01 2lhb 149 -14.20 -5.31 1.17e+01 1m6dA 214 -13.62 -5.31 1.18e+01 2f96A 224 -13.67 -5.30 1.19e+01 1yw0A 276 -15.37 -5.28 1.21e+01 1f07A 321 -14.41 -5.27 1.22e+01 1ovnA 248 -14.05 -5.18 1.32e+01 1vk9A 151 -13.53 -5.10 1.42e+01 1tueB 218 -13.72 -5.09 1.44e+01 1qrqA 325 -13.84 -5.03 1.52e+01 1jeyB 565 -13.96 -5.02 1.53e+01 1su4A 994 -15.40 -5.01 1.56e+01 1r5zA 323 -13.88 -4.98 1.59e+01 3pbgA 468 -13.81 -4.98 1.60e+01 1ak0 270 -14.07 -4.98 1.60e+01 1jeqB 565 -13.96 -4.97 1.61e+01 1n2sA 299 -13.27 -4.89 1.74e+01 1pbgA 468 -13.81 -4.82 1.85e+01 1lfdA 87 -12.24 -4.81 1.88e+01 1wpgA 994 -15.34 -4.68 2.11e+01 1bg6 359 -13.57 -4.64 2.21e+01 1hcc 59 -11.57 -4.62 2.25e+01 1b4fG 82 -13.28 -4.62 2.26e+01 1ws6A 171 -12.73 -4.60 2.29e+01 1m2eA 135 -12.33 -4.59 2.32e+01 1s4bP 674 -13.96 -4.52 2.47e+01 1f88A 348 -14.42 -4.51 2.49e+01 1ll2A 333 -13.08 -4.50 2.52e+01 1t0qA 498 -13.55 -4.48 2.58e+01 1ash 150 -13.63 -4.48 2.58e+01 1b4fA 82 -13.21 -4.47 2.59e+01 1qhtA 775 -13.70 -4.47 2.60e+01 1oya 400 -13.47 -4.45 2.65e+01 1wwpA 119 -15.16 -4.43 2.70e+01 2c3vA 102 -11.61 -4.42 2.73e+01 1oyc 400 -13.44 -4.42 2.73e+01 1f0mA 82 -13.07 -4.41 2.74e+01 1rzl 91 -13.08 -4.40 2.77e+01 1tbfA 347 -13.57 -4.39 2.81e+01 1ll0A 339 -12.98 -4.36 2.90e+01 1bx4A 345 -13.02 -4.35 2.92e+01 1b25A 619 -13.42 -4.34 2.94e+01 1lxdA 100 -11.75 -4.33 2.96e+01 1z3xA 238 -13.68 -4.33 2.98e+01 1lj8A 493 -12.90 -4.32 3.00e+01 1u5tA 233 -13.38 -4.30 3.06e+01 1tgoA 773 -13.84 -4.23 3.28e+01 1hqkA 154 -13.20 -4.22 3.31e+01 1k9tA 540 -12.78 -4.20 3.36e+01 1zsyA 357 -13.00 -4.20 3.38e+01 1edqA 540 -12.79 -4.18 3.45e+01 1dmtA 696 -14.10 -4.18 3.46e+01 3adk 195 -12.95 -4.16 3.51e+01 1r1hA 696 -14.09 -4.13 3.63e+01 1oyb 400 -13.13 -4.12 3.65e+01 1m3yA 413 -11.68 -4.09 3.76e+01 2bykA 140 -12.79 -4.08 3.81e+01 1o51A 114 -11.90 -4.06 3.89e+01 1nktA 922 -14.17 -4.03 3.99e+01 1a17 166 -13.01 -4.03 3.99e+01