% 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. % --------------------------------------------------------------------- % dsspfoo.1.YGR227W.t2k-100-30-dssp-ebghstl Host: cc34 Tue Nov 12 18:30:05 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-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 526 nodes, 370.53 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(=1.8364) * Reverse)^tau(=0.7161))) % 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 1jjuA 489 -36.88 -11.99 7.75e-01 1kyoC 385 -47.11 -11.25 1.17e+00 1ezvC 385 -46.14 -10.51 1.77e+00 1i5pA 633 -41.64 -9.98 2.40e+00 1qi7A 253 -32.78 -9.85 2.58e+00 1lmzA 187 -34.13 -9.79 2.67e+00 1hg5A 289 -39.26 -9.41 3.32e+00 1hg2A 289 -38.97 -9.41 3.33e+00 1iw7C 1119 -38.33 -9.32 3.51e+00 1hf8A 289 -38.84 -9.29 3.58e+00 1e8yA 966 -42.99 -8.98 4.30e+00 1qlaC 256 -46.91 -8.96 4.33e+00 1c4zA 358 -34.13 -8.84 4.65e+00 1csh 435 -40.01 -8.57 5.48e+00 1lshA 1056 -39.63 -8.33 6.33e+00 1gk4A 84 -33.22 -8.27 6.58e+00 1amz 435 -39.90 -8.14 7.12e+00 1qb4A 883 -41.82 -7.94 8.05e+00 3blm 257 -31.33 -7.90 8.22e+00 1ghpA 258 -31.48 -7.87 8.41e+00 1pioA 257 -31.39 -7.80 8.74e+00 1csc 433 -38.50 -7.74 9.06e+00 1fiy 883 -41.45 -7.72 9.18e+00 1l9hA 349 -42.82 -7.63 9.75e+00 1qazA 351 -41.97 -7.58 1.00e+01 1f5qB 252 -35.86 -7.57 1.01e+01 1h6oA 204 -34.17 -7.47 1.07e+01 1dekA 241 -32.67 -7.47 1.08e+01 6cts 433 -38.18 -7.44 1.10e+01 1fmcA 255 -32.01 -7.39 1.13e+01 1ecxA 384 -31.89 -7.34 1.17e+01 1qtrA 317 -32.04 -7.26 1.22e+01 1gkuB 1054 -35.82 -7.13 1.33e+01 1itf 165 -34.52 -7.10 1.35e+01 1jmeA 455 -38.33 -7.07 1.38e+01 1ezfA 340 -39.87 -7.00 1.44e+01 1alq 266 -30.16 -6.95 1.49e+01 1e8xA 961 -42.43 -6.94 1.50e+01 1eg5A 384 -31.75 -6.93 1.51e+01 1hw1A 239 -34.50 -6.90 1.54e+01 1ko9A 345 -30.66 -6.88 1.56e+01 1eu1A 780 -33.00 -6.87 1.57e+01 1bk5A 422 -37.25 -6.84 1.60e+01 1dmtA 696 -38.82 -6.84 1.60e+01 2cblA 305 -37.03 -6.73 1.71e+01 1bgj 394 -35.03 -6.69 1.76e+01 1k3lA 221 -35.93 -6.69 1.76e+01 1pbe 394 -34.83 -6.64 1.82e+01 1gk4D 84 -31.11 -6.59 1.89e+01 1jeqA 609 -31.22 -6.51 1.98e+01 1avc 673 -40.03 -6.50 1.99e+01 1cleA 534 -31.65 -6.50 1.99e+01 1dcnA 424 -39.50 -6.49 2.00e+01 1e2xA 243 -34.68 -6.46 2.05e+01 1hzxA 349 -42.30 -6.45 2.06e+01 1fnnA 389 -32.26 -6.43 2.09e+01 1qsaA 618 -37.44 -6.42 2.10e+01 1gdeA 389 -30.14 -6.39 2.14e+01 1fftC 204 -36.99 -6.35 2.20e+01 1jeyA 609 -31.41 -6.34 2.21e+01 1gd9A 389 -30.04 -6.29 2.29e+01 1delA 241 -31.46 -6.28 2.30e+01 1i7gA 287 -36.84 -6.26 2.32e+01 1gseA 221 -35.51 -6.26 2.33e+01 1eyhA 144 -33.72 -6.24 2.36e+01 1eduA 149 -33.80 -6.19 2.44e+01 1g73A 162 -37.24 -6.18 2.45e+01 1ixmB 192 -32.92 -6.16 2.49e+01 2phh 394 -34.29 -6.15 2.50e+01 1efvB 255 -27.84 -6.12 2.55e+01 1qpcA 279 -29.38 -6.11 2.57e+01 1inzA 148 -31.73 -6.02 2.72e+01 1f88A 348 -41.53 -6.01 2.74e+01 1wer 334 -35.74 -6.00 2.76e+01 2minB 522 -33.35 -5.98 2.81e+01 1ezvB 352 -29.49 -5.97 2.82e+01 1fewA 184 -37.81 -5.92 2.91e+01 1h3nA 878 -36.01 -5.92 2.92e+01 1g0oA 283 -31.60 -5.89 2.98e+01 1ee4A 423 -37.06 -5.87 3.01e+01 1e19A 314 -32.35 -5.87 3.02e+01 1fi2A 201 -26.74 -5.86 3.04e+01 2dubE 261 -29.56 -5.85 3.05e+01 1k0iA 394 -34.59 -5.85 3.06e+01 1ast 200 -26.48 -5.84 3.07e+01 1iae 200 -26.48 -5.84 3.07e+01 1bk6A 422 -36.44 -5.81 3.14e+01 1b47A 304 -36.62 -5.80 3.16e+01 1dcqA 278 -31.82 -5.76 3.25e+01 1fzyA 149 -27.98 -5.75 3.26e+01 1b3uA 588 -37.53 -5.74 3.29e+01 1f60A 458 -30.99 -5.71 3.36e+01 1jqhA 308 -29.08 -5.70 3.38e+01 3lck 271 -29.15 -5.70 3.38e+01 1g4yB 101 -29.76 -5.69 3.39e+01 3minB 522 -33.17 -5.68 3.43e+01 1iab 200 -26.29 -5.65 3.50e+01 1hbnB 442 -33.80 -5.64 3.53e+01 1dw9A 156 -28.56 -5.63 3.55e+01 1quvA 578 -31.89 -5.61 3.59e+01 1ybvA 283 -31.29 -5.60 3.60e+01 2occE 109 -28.59 -5.59 3.65e+01 1js3A 486 -31.83 -5.58 3.66e+01 1io1A 398 -42.64 -5.57 3.68e+01 1ps1A 337 -36.54 -5.57 3.68e+01 1g94A 448 -29.50 -5.55 3.74e+01 1fxtA 149 -27.87 -5.55 3.75e+01 1jscA 630 -31.43 -5.52 3.81e+01 1ebmA 317 -29.32 -5.52 3.82e+01 1mroB 442 -33.66 -5.50 3.87e+01 1gkmA 509 -34.48 -5.47 3.93e+01 1ixmA 192 -31.29 -5.47 3.94e+01 1br2A 791 -33.14 -5.47 3.94e+01 1dcnD 436 -39.06 -5.46 3.96e+01