% 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. % --------------------------------------------------------------------- % stridefoo.1.YGR013W.t2k-100-30-stride-ebghtl Host: farm09.cse.ucsc.edu Sun Mar 19 22:13:37 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR013W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds % % 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 YGR013W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR013W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 621 nodes, 1024.20 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(=1.2313) * Reverse)^tau(=0.7932))) % 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 1m6yA 301 -30.89 -16.15 2.44e-01 1l8qA 324 -29.33 -12.13 2.15e+00 1de4C 640 -28.01 -12.13 2.16e+00 1mp1A 111 -24.17 -11.98 2.35e+00 1wa5C 960 -35.28 -11.64 2.83e+00 1jbwA 428 -23.99 -11.55 2.97e+00 1fgs 428 -24.21 -11.49 3.09e+00 1twfA 1733 -27.64 -11.42 3.20e+00 6tmnE 316 -26.19 -11.37 3.29e+00 1f6dA 376 -25.19 -11.32 3.39e+00 1keiA 316 -26.35 -11.02 4.04e+00 1vgvA 384 -24.87 -10.98 4.11e+00 1uuqA 440 -24.15 -10.98 4.13e+00 1hyt 316 -26.27 -10.87 4.39e+00 8tlnE 316 -26.27 -10.87 4.39e+00 1cb8A 678 -24.80 -10.63 5.02e+00 2tmnE 316 -26.26 -10.63 5.03e+00 1k28A 584 -25.36 -10.43 5.63e+00 2ts1 419 -28.06 -10.33 5.99e+00 1i50A 1733 -26.72 -10.27 6.17e+00 1zkiA 133 -21.50 -10.17 6.57e+00 1wovA 250 -27.58 -10.11 6.79e+00 1lzlA 323 -22.85 -9.97 7.35e+00 1gvfA 286 -23.61 -9.83 7.97e+00 2basA 431 -23.62 -9.81 8.08e+00 1pgjA 478 -24.62 -9.77 8.26e+00 1hm2A 700 -23.32 -9.67 8.77e+00 1wxcA 281 -22.76 -9.39 1.03e+01 2f02A 323 -21.75 -9.25 1.12e+01 2cvxA 888 -23.43 -9.23 1.13e+01 1t6jA 714 -23.31 -9.18 1.17e+01 2awdA 323 -21.57 -8.98 1.31e+01 1ynmA 247 -22.42 -8.93 1.36e+01 2fkcA 247 -22.43 -8.93 1.36e+01 2d7vA 162 -21.72 -8.84 1.43e+01 16vpA 366 -26.82 -8.78 1.48e+01 1jqiA 388 -21.41 -8.70 1.56e+01 2bneA 241 -21.32 -8.68 1.57e+01 1mu5A 471 -23.18 -8.63 1.62e+01 1js3A 486 -22.15 -8.59 1.66e+01 2hgsA 474 -22.02 -8.56 1.69e+01 1clxA 347 -21.01 -8.55 1.70e+01 1sqsA 242 -21.99 -8.47 1.78e+01 1sxrA 183 -20.72 -8.45 1.81e+01 1d8cA 723 -23.20 -8.43 1.83e+01 1lehA 364 -22.74 -8.37 1.89e+01 2cq2A 114 -18.87 -8.36 1.90e+01 1jgcA 161 -28.78 -8.33 1.94e+01 1w32A 348 -20.79 -8.32 1.95e+01 1b9hA 388 -25.30 -8.32 1.95e+01 1e5rA 290 -22.92 -8.23 2.06e+01 2es4D 332 -26.86 -8.15 2.17e+01 1rzuA 485 -20.54 -8.12 2.20e+01 1rkeA 262 -26.76 -8.11 2.21e+01 1e4mM 501 -23.98 -8.09 2.24e+01 1ukvY 206 -20.48 -8.07 2.27e+01 1wmaA 276 -23.76 -8.05 2.30e+01 1qdbA 473 -26.22 -8.00 2.37e+01 1j0hA 588 -22.60 -7.98 2.39e+01 1y6iA 233 -21.66 -7.96 2.43e+01 1b1yA 500 -22.37 -7.94 2.46e+01 2bcgY 206 -20.31 -7.92 2.49e+01 1sqc 631 -25.62 -7.91 2.51e+01 1va6A 518 -23.08 -7.90 2.53e+01 1tpt 440 -21.06 -7.88 2.55e+01 2sqcA 631 -25.62 -7.86 2.58e+01 1uruA 244 -28.58 -7.86 2.58e+01 1wmwA 330 -26.08 -7.81 2.66e+01 1nxuA 333 -20.76 -7.78 2.72e+01 137lA 164 -21.93 -7.77 2.73e+01 1x8yA 86 -24.35 -7.73 2.80e+01 1z23A 163 -22.15 -7.70 2.84e+01 2al6A 375 -22.91 -7.69 2.87e+01 1r8iA 213 -24.12 -7.66 2.91e+01 1m0kA 262 -21.67 -7.66 2.91e+01 1ydiA 263 -26.93 -7.65 2.94e+01 1y2mA 716 -22.19 -7.63 2.97e+01 1v58A 241 -19.24 -7.62 2.98e+01 1lkcA 364 -20.19 -7.62 2.99e+01 1kgbA 231 -21.54 -7.61 3.02e+01 1jqzA 146 -18.22 -7.60 3.02e+01 1m16A 146 -18.41 -7.59 3.04e+01 1e6qM 501 -23.98 -7.58 3.06e+01 180lA 164 -21.28 -7.57 3.08e+01 139l 164 -21.80 -7.54 3.13e+01 2az4A 429 -22.33 -7.50 3.23e+01 1rg8A 146 -18.11 -7.49 3.23e+01 1jt7A 146 -18.20 -7.48 3.26e+01 1k4tA 592 -25.03 -7.47 3.27e+01 1f6yA 262 -20.49 -7.47 3.28e+01 1klfB 279 -18.68 -7.45 3.31e+01 1itcA 516 -22.88 -7.44 3.34e+01 1sfkA 76 -19.53 -7.43 3.36e+01 1nq6A 302 -19.60 -7.41 3.39e+01 2at9 247 -20.77 -7.39 3.44e+01 1dqaA 467 -20.13 -7.39 3.45e+01 1qhbA 596 -21.75 -7.36 3.50e+01 1arzC 273 -20.68 -7.36 3.51e+01 1o60A 292 -21.19 -7.36 3.51e+01 1u6zA 513 -21.38 -7.34 3.55e+01 1iv8A 720 -26.77 -7.33 3.57e+01 2acvA 463 -21.94 -7.33 3.57e+01 1dqaC 467 -20.02 -7.32 3.59e+01 1ev0A 58 -18.60 -7.30 3.64e+01 1hw8A 467 -20.09 -7.29 3.67e+01 1xngA 268 -23.81 -7.27 3.70e+01 1gmlA 178 -21.21 -7.26 3.72e+01 1lc5A 364 -20.33 -7.26 3.73e+01 1tq4A 413 -24.96 -7.25 3.76e+01 2cujA 108 -20.14 -7.18 3.93e+01 1dih 273 -20.44 -7.16 3.96e+01