% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR227W.t2k-100-30-dssp-ehl2 Host: cc34 Tue Nov 12 19:06:39 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR227W % --------------------------------------------------------------------- % 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 ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR227W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR227W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 526 nodes, 377.77 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 (=7316) sequences: % N / (1 + exp(-(lambda(=1.9012) * Reverse)^tau(=0.7309))) % 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 1csh 435 -42.64 -12.40 3.09e-01 1amz 435 -42.60 -12.18 3.52e-01 1iw7C 1119 -40.10 -10.96 7.37e-01 1csc 433 -40.31 -10.44 1.02e+00 1pbe 394 -36.49 -10.05 1.30e+00 1bgj 394 -36.39 -9.92 1.40e+00 1k0iA 394 -36.84 -9.82 1.50e+00 2phh 394 -35.91 -9.47 1.87e+00 6cts 433 -39.23 -9.45 1.90e+00 1lmzA 187 -33.52 -9.45 1.90e+00 1c4zA 358 -34.32 -9.25 2.15e+00 1jjuA 489 -33.73 -8.24 4.16e+00 1rpa 342 -33.33 -8.19 4.30e+00 1dmtA 696 -39.62 -8.00 4.89e+00 1jmeA 455 -37.48 -7.51 6.80e+00 1quvA 578 -34.16 -7.25 8.12e+00 1gk4A 84 -30.73 -7.22 8.29e+00 1qi7A 253 -29.57 -7.14 8.74e+00 1scfA 273 -32.92 -7.09 9.02e+00 1k3lA 221 -34.35 -6.99 9.71e+00 1dw9A 156 -29.87 -6.98 9.75e+00 2cblA 305 -34.87 -6.92 1.02e+01 1fi2A 201 -28.20 -6.90 1.03e+01 1eu1A 780 -33.41 -6.88 1.04e+01 1qtrA 317 -31.44 -6.82 1.09e+01 1gseA 221 -34.10 -6.82 1.09e+01 1gx5A 536 -33.34 -6.68 1.20e+01 1fiy 883 -39.01 -6.59 1.28e+01 1h6oA 204 -33.28 -6.52 1.35e+01 1b47A 304 -34.90 -6.50 1.37e+01 1exzA 141 -30.18 -6.46 1.41e+01 1jpzA 473 -36.79 -6.38 1.48e+01 1d6mA 653 -32.53 -6.38 1.48e+01 1qb4A 883 -38.66 -6.38 1.49e+01 2minB 522 -33.92 -6.28 1.59e+01 1jeqA 609 -32.25 -6.19 1.70e+01 1ecxA 384 -30.13 -6.15 1.75e+01 1i5pA 633 -37.50 -6.13 1.78e+01 1ihp 438 -32.72 -6.12 1.78e+01 1fnnA 389 -32.11 -6.12 1.79e+01 1c2pA 576 -33.15 -6.09 1.83e+01 1ko9A 345 -30.37 -6.07 1.85e+01 4cpv 109 -26.82 -6.06 1.86e+01 1hp5A 512 -30.07 -6.02 1.92e+01 1eg5A 384 -30.43 -6.02 1.92e+01 1dwkA 156 -29.95 -6.02 1.93e+01 1qrkA 731 -30.95 -6.01 1.94e+01 2bmhA 455 -37.79 -6.01 1.94e+01 1dysA 348 -29.68 -5.99 1.96e+01 1jakA 512 -30.07 -5.99 1.96e+01 1gguA 731 -30.91 -5.95 2.02e+01 3minB 522 -33.92 -5.89 2.11e+01 1itf 165 -31.65 -5.88 2.12e+01 1gk4D 84 -28.88 -5.87 2.14e+01 1hp4A 512 -29.82 -5.80 2.26e+01 1cdp 109 -26.50 -5.78 2.29e+01 1fewA 184 -34.82 -5.73 2.38e+01 1g8lA 411 -28.78 -5.72 2.38e+01 1g73A 162 -34.31 -5.72 2.40e+01 1f5qB 252 -32.93 -5.71 2.40e+01 1cleA 534 -31.53 -5.69 2.44e+01 1ebmA 317 -30.02 -5.68 2.45e+01 1dbhA 354 -34.31 -5.68 2.46e+01 1jmkC 230 -27.36 -5.59 2.62e+01 1qs0A 407 -31.12 -5.59 2.63e+01 1rlr 761 -33.28 -5.53 2.74e+01 1kcfA 258 -31.60 -5.52 2.76e+01 1csjA 531 -32.39 -5.51 2.79e+01 1dmr 823 -32.01 -5.50 2.81e+01 1ckiA 317 -30.36 -5.49 2.83e+01 1gkmA 509 -32.71 -5.49 2.83e+01 1db1A 259 -31.47 -5.46 2.90e+01 1eq2A 310 -28.91 -5.42 2.98e+01 1evuA 731 -30.51 -5.42 2.98e+01 1ldjA 760 -37.29 -5.39 3.04e+01 1jvpP 298 -29.25 -5.39 3.05e+01 1hg2A 289 -32.95 -5.32 3.20e+01 1kyhA 276 -29.38 -5.32 3.20e+01 1f13A 731 -30.30 -5.32 3.21e+01 1fmcA 255 -29.78 -5.31 3.23e+01 1fe0A 68 -25.30 -5.29 3.27e+01 1jm6A 407 -37.73 -5.23 3.43e+01 1jqhA 308 -28.85 -5.22 3.46e+01 1e1xA 299 -28.93 -5.21 3.49e+01 1dar 691 -30.96 -5.18 3.55e+01 1jeyA 609 -31.49 -5.16 3.61e+01 1isaA 192 -27.53 -5.15 3.64e+01 1iscA 192 -27.53 -5.15 3.65e+01 1hf8A 289 -33.02 -5.13 3.69e+01 1eyhA 144 -30.53 -5.11 3.76e+01 1gdeA 389 -28.87 -5.10 3.76e+01 2ebn 289 -27.79 -5.09 3.80e+01 1dcnA 424 -37.07 -5.08 3.84e+01 1eduA 149 -30.59 -5.07 3.87e+01