% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 09/03/03_16:30:36 % (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.YGR212W.t2k-100-30-stride-ebghtl Host: cc50 Sun Oct 12 01:03:52 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR212W % --------------------------------------------------------------------- % 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 ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR212W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR212W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 469 nodes, 437.11 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 (=8162) sequences: % N / (1 + exp(-(lambda(=1.2583) * Reverse)^tau(=0.8502))) % 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 1l5aA 436 -38.98 -14.86 4.74e-02 8pchA 220 -34.15 -12.05 3.39e-01 1lnsA 763 -37.36 -11.36 5.56e-01 1i19A 561 -35.55 -10.69 8.98e-01 2minB 522 -34.49 -10.11 1.37e+00 1mkiA 330 -33.34 -9.86 1.64e+00 1keiA 316 -32.62 -9.84 1.67e+00 2tmnE 316 -32.60 -9.80 1.73e+00 1hyt 316 -32.57 -9.75 1.79e+00 8tlnE 316 -32.57 -9.75 1.79e+00 6tmnE 316 -32.62 -9.73 1.81e+00 1m1nB 522 -34.12 -9.55 2.07e+00 1bgp 309 -31.95 -9.35 2.39e+00 1h2aL 567 -33.52 -9.20 2.67e+00 1azo 232 -31.59 -9.13 2.81e+00 1el6A 219 -32.27 -8.90 3.36e+00 1el6B 219 -32.36 -8.80 3.60e+00 1cxqA 162 -30.78 -8.70 3.89e+00 3minB 522 -33.41 -8.30 5.24e+00 1amj 754 -34.31 -8.26 5.41e+00 8acn 754 -34.30 -8.24 5.49e+00 1ubkL 534 -32.41 -8.07 6.25e+00 1vsd 152 -30.43 -8.02 6.48e+00 2kinA 238 -31.61 -7.98 6.66e+00 1jvpP 298 -31.99 -7.98 6.70e+00 1gsoA 431 -33.03 -7.97 6.75e+00 1asu 162 -30.43 -7.81 7.58e+00 1f5mA 180 -31.01 -7.81 7.59e+00 1h2rL 534 -32.07 -7.77 7.81e+00 1gtkA 313 -30.30 -7.73 8.09e+00 1pda 315 -30.34 -7.72 8.13e+00 1g4uS 383 -32.41 -7.66 8.52e+00 1f5mB 180 -30.92 -7.63 8.70e+00 1b0jA 754 -34.06 -7.50 9.62e+00 1g4wR 383 -33.15 -7.46 9.91e+00 1gqeA 365 -31.19 -7.45 9.96e+00 1k6xA 352 -31.71 -7.39 1.05e+01 1fljA 260 -31.11 -7.33 1.10e+01 1k6iA 352 -31.86 -7.30 1.12e+01 1e3dB 542 -31.16 -7.27 1.14e+01 7acn 754 -33.86 -7.27 1.15e+01 1hcl 298 -31.06 -7.09 1.31e+01 1c96A 753 -33.86 -7.06 1.35e+01 1uc8A 280 -29.41 -7.01 1.40e+01 1oe4A 247 -31.15 -7.00 1.41e+01 1gz8A 299 -30.77 -6.87 1.56e+01 1icxA 155 -32.87 -6.82 1.62e+01 1g8fA 511 -32.36 -6.70 1.78e+01 1cby 259 -30.25 -6.68 1.81e+01 1a3c 181 -32.31 -6.57 1.97e+01 6acn 754 -33.40 -6.52 2.05e+01 1qo7A 394 -30.54 -6.50 2.08e+01 1kf6B 243 -28.53 -6.49 2.10e+01 1gskA 513 -31.63 -6.44 2.18e+01 1qcsA 211 -29.37 -6.33 2.38e+01 1bg2 325 -30.67 -6.31 2.41e+01 1ni4B 341 -29.55 -6.29 2.44e+01 1e1xA 299 -30.71 -6.28 2.46e+01 1f8rA 498 -31.19 -6.26 2.52e+01 1a15A 67 -26.37 -6.25 2.52e+01 1nf3C 128 -26.24 -6.24 2.54e+01 1f1sA 814 -33.26 -6.24 2.56e+01 1cx4A 305 -28.57 -6.19 2.65e+01 1go2A 304 -29.88 -6.17 2.68e+01 3ldh 330 -28.43 -6.15 2.74e+01 1bk1 184 -28.89 -6.10 2.85e+01 1ipaA 274 -28.43 -6.08 2.89e+01 1eysH 259 -29.47 -6.04 2.97e+01 1h3gA 601 -30.90 -6.02 3.02e+01 1dq3A 454 -33.08 -6.00 3.08e+01 1e2kA 331 -30.00 -5.89 3.35e+01 1brt 277 -28.77 -5.87 3.41e+01 1kxoA 184 -29.38 -5.86 3.45e+01 1jkgA 140 -29.52 -5.79 3.62e+01 1aol 228 -27.45 -5.75 3.74e+01 1lbvA 252 -29.26 -5.70 3.88e+01 2ki5A 366 -29.35 -5.70 3.90e+01 1smd 496 -30.69 -5.68 3.96e+01