% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-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.YGR009C.t2k-100-30-stride-ebghtl Host: farm20 Wed Nov 17 16:56:41 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR009C % --------------------------------------------------------------------- % 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 YGR009C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR009C.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10772 sequences, 2550165 residues, 652 nodes, 700.71 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 (=10700) sequences: % N / (1 + exp(-(lambda(=0.9961) * Reverse)^tau(=0.8417))) % 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 1sfcC 83 -108.02 -86.69 3.27e-15 1n7sC 79 -107.64 -86.52 3.52e-15 1l4aD 87 -102.62 -83.21 1.39e-14 1sfcD 87 -108.29 -83.11 1.45e-14 1jthA 82 -100.31 -77.90 1.28e-13 1kilD 66 -99.90 -74.56 5.26e-13 1n7sD 66 -99.90 -74.55 5.29e-13 1gl2C 65 -67.14 -51.65 1.14e-08 1gl2D 65 -69.47 -46.39 1.23e-07 1n7sB 68 -40.53 -21.49 2.02e-02 1hvvA 75 -40.48 -21.06 2.52e-02 1sfcB 83 -40.89 -21.06 2.52e-02 1jthB 77 -40.47 -20.71 3.02e-02 1jthD 77 -38.04 -20.49 3.39e-02 1gl2B 65 -39.50 -20.37 3.60e-02 1xsm 390 -31.84 -15.04 6.17e-01 1h0oA 390 -31.54 -14.18 9.90e-01 1dn1B 267 -41.53 -14.16 9.98e-01 1tqhA 247 -27.82 -14.01 1.08e+00 1icpA 376 -28.49 -13.34 1.57e+00 1w68A 390 -30.03 -13.20 1.71e+00 1s35A 214 -29.17 -12.91 2.00e+00 1k7wA 468 -30.28 -12.54 2.47e+00 1r1dA 247 -25.40 -12.06 3.22e+00 1ni3A 392 -27.26 -11.99 3.36e+00 1jadA 251 -36.29 -11.89 3.57e+00 1ih7A 903 -28.28 -11.74 3.88e+00 1oxjA 173 -25.97 -11.72 3.91e+00 1jeyB 565 -28.37 -11.53 4.37e+00 1qwlA 505 -30.51 -11.35 4.84e+00 1jeqB 565 -28.78 -11.25 5.12e+00 1k92A 455 -24.49 -10.72 6.95e+00 1gy8A 397 -22.72 -10.33 8.69e+00 1kv7A 488 -25.24 -10.31 8.82e+00 1k47A 337 -24.73 -10.29 8.89e+00 1i50C 318 -24.70 -10.12 9.80e+00 1lvoA 302 -28.22 -10.02 1.04e+01 1clqA 903 -28.22 -9.92 1.10e+01 1s4nA 348 -23.43 -9.87 1.13e+01 1auwA 468 -28.52 -9.87 1.13e+01 1bt3A 345 -29.43 -9.81 1.18e+01 1hy0A 466 -26.65 -9.76 1.21e+01 2tysB 397 -23.33 -9.71 1.25e+01 2wsyB 396 -23.50 -9.70 1.25e+01 1v8gA 329 -22.51 -9.67 1.27e+01 1k8yB 396 -24.08 -9.61 1.33e+01 1jqiA 388 -23.38 -9.58 1.35e+01 1qopB 396 -23.78 -9.54 1.38e+01 1gln 468 -23.95 -9.46 1.44e+01 1kjvA 284 -24.34 -9.45 1.45e+01 1chuA 540 -26.86 -9.44 1.46e+01 1wduA 245 -22.31 -9.43 1.47e+01 1bksB 397 -22.78 -9.36 1.53e+01 1umwA 237 -23.55 -9.33 1.56e+01 1sziA 247 -29.45 -9.19 1.70e+01 1txuA 273 -24.26 -9.16 1.72e+01 1ewqA 765 -25.89 -9.04 1.85e+01 1o5kA 306 -24.89 -8.91 2.00e+01 1fxkB 109 -29.79 -8.88 2.04e+01 1nc5A 373 -24.47 -8.78 2.16e+01 1qg0A 308 -23.45 -8.77 2.16e+01 1nfiC 301 -23.16 -8.77 2.18e+01 1g59A 468 -23.34 -8.71 2.24e+01 1knvA 293 -21.71 -8.70 2.26e+01 1j09A 468 -23.30 -8.70 2.27e+01 3erdA 261 -26.02 -8.69 2.28e+01 1ttuA 477 -22.96 -8.68 2.29e+01 1bg7 176 -24.60 -8.68 2.29e+01 1dxrL 273 -25.02 -8.51 2.54e+01 1keyA 235 -27.90 -8.51 2.54e+01 4gr1 478 -22.40 -8.43 2.65e+01 1ic2A 81 -28.33 -8.42 2.67e+01 1xfjA 261 -20.25 -8.40 2.71e+01 3grs 478 -22.48 -8.31 2.86e+01 1pmmA 466 -25.18 -8.27 2.92e+01 1nfiA 301 -22.57 -8.27 2.93e+01 1q33A 292 -22.03 -8.23 3.00e+01 1spa 396 -20.77 -8.23 3.00e+01 1f82A 424 -25.79 -8.21 3.02e+01 5csmA 256 -28.00 -8.20 3.06e+01 1dcnD 436 -25.30 -8.15 3.13e+01 1q4gA 553 -25.07 -8.15 3.15e+01 1qisA 396 -21.00 -8.13 3.18e+01 7catA 506 -28.07 -8.12 3.21e+01 1art 396 -20.98 -8.10 3.24e+01 1ahxA 396 -20.80 -8.09 3.25e+01 2aat 396 -22.06 -8.09 3.27e+01 1m3vA 122 -21.55 -7.99 3.47e+01 1ars 396 -20.65 -7.98 3.47e+01 1fm9D 272 -22.41 -7.89 3.67e+01 1uahA 431 -22.55 -7.88 3.70e+01 1ug6A 431 -22.55 -7.87 3.71e+01 1f83A 425 -24.71 -7.86 3.73e+01 1vcaA 202 -19.04 -7.83 3.81e+01 1igtD 444 -21.28 -7.81 3.85e+01 2prgA 271 -22.42 -7.80 3.89e+01