% 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. % --------------------------------------------------------------------- % strfoo.1.YGR023W.t2k-100-30-str Host: cc66 Fri Dec 13 16:44:32 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR023W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.strs % % 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 YGR023W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR023W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7458 sequences, 1753770 residues, 552 nodes, 387.06 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(=1.4258) * Reverse)^tau(=0.8132))) % 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 1d0nA 729 -39.48 -11.26 5.17e-01 1jk7A 323 -35.29 -10.81 7.05e-01 6prcH 258 -38.77 -10.12 1.15e+00 1dxrH 258 -38.22 -9.75 1.49e+00 1fjmA 330 -34.30 -9.57 1.69e+00 1f28A 297 -33.15 -9.13 2.31e+00 1cx8B 639 -37.83 -8.40 3.93e+00 1bqhG 129 -37.00 -8.08 4.94e+00 1aim 215 -32.99 -8.06 5.03e+00 1gqpA 221 -32.89 -8.05 5.07e+00 1azsA 220 -29.97 -8.01 5.23e+00 1khbA 625 -36.67 -7.93 5.52e+00 1dgjA 907 -34.78 -7.84 5.92e+00 1ciy 590 -43.58 -7.80 6.07e+00 1ksiB 642 -38.95 -7.73 6.39e+00 1ej6A 1289 -42.17 -7.69 6.58e+00 1ehkB 168 -33.39 -7.68 6.68e+00 1itkA 731 -34.84 -7.67 6.71e+00 1culA 217 -29.17 -7.61 7.03e+00 1qvcA 145 -30.57 -7.51 7.53e+00 1je0A 236 -28.47 -7.42 8.05e+00 2rmpA 361 -41.75 -7.38 8.33e+00 1spuB 727 -36.84 -7.36 8.43e+00 1gctA 245 -39.69 -7.34 8.54e+00 1e2tA 284 -32.24 -7.32 8.68e+00 3aprE 325 -34.14 -7.29 8.86e+00 1cjtA 217 -29.11 -7.28 8.94e+00 1cxlA 686 -41.91 -7.27 9.03e+00 1jmxA 494 -35.61 -7.26 9.11e+00 2sqcA 631 -32.26 -7.23 9.28e+00 1cx8A 639 -37.42 -7.22 9.36e+00 1ksiA 642 -38.62 -7.21 9.46e+00 1k6dA 220 -29.21 -7.19 9.61e+00 1f2aA 215 -32.13 -7.13 1.01e+01 1kawA 135 -28.64 -7.11 1.02e+01 1sqc 631 -32.11 -7.08 1.04e+01 1qovH 260 -36.93 -7.08 1.04e+01 2apr 325 -34.13 -7.03 1.08e+01 1de4C 640 -34.24 -6.98 1.12e+01 1d3cA 686 -42.56 -6.96 1.14e+01 1jjuB 337 -36.87 -6.95 1.15e+01 1vhrA 184 -27.41 -6.91 1.18e+01 1eysH 259 -39.48 -6.88 1.21e+01 1k42A 168 -34.55 -6.79 1.30e+01 2bbkH 355 -36.52 -6.75 1.33e+01 1qoiA 177 -30.54 -6.71 1.37e+01 1soxA 466 -33.94 -6.59 1.51e+01 1eaf 243 -29.46 -6.55 1.55e+01 1k4mA 213 -27.42 -6.53 1.58e+01 1eu1A 780 -35.50 -6.53 1.58e+01 1oacA 727 -36.09 -6.53 1.58e+01 1ktbA 405 -32.45 -6.53 1.58e+01 1qh4A 380 -32.08 -6.44 1.69e+01 1d6zA 727 -35.87 -6.29 1.90e+01 1f00I 282 -38.75 -6.28 1.91e+01 1gg6B 131 -34.14 -6.20 2.03e+01 1jr3E 334 -29.12 -6.20 2.03e+01 2asi 360 -42.56 -6.19 2.05e+01 1m56B 264 -31.69 -6.18 2.06e+01 2eifA 136 -33.01 -6.15 2.12e+01 1d4bA 122 -31.21 -6.06 2.26e+01 1k32A 1045 -43.11 -6.05 2.27e+01 1et0A 269 -31.30 -6.05 2.29e+01 1l9mA 692 -38.88 -6.02 2.34e+01 1tx4B 178 -26.87 -6.02 2.34e+01 1aqjA 421 -30.72 -5.83 2.71e+01 1f0lA 535 -34.69 -5.76 2.86e+01 2dhqA 146 -27.80 -5.70 2.99e+01 1lrzA 426 -29.06 -5.69 3.02e+01 1dpb 243 -28.47 -5.64 3.15e+01 1j9qA 341 -31.25 -5.63 3.16e+01 1et7A 341 -31.49 -5.62 3.18e+01 1a5t 334 -28.31 -5.60 3.23e+01 1h05A 146 -27.78 -5.60 3.24e+01 1avk 638 -37.48 -5.58 3.28e+01 1tdj 514 -29.04 -5.58 3.30e+01 1dpgA 485 -29.86 -5.56 3.34e+01 1pmi 440 -33.76 -5.56 3.34e+01 1dim 381 -38.94 -5.55 3.38e+01 1goiA 499 -30.38 -5.52 3.45e+01 1b43A 340 -28.71 -5.47 3.59e+01 1ek8A 185 -27.23 -5.44 3.67e+01 1e6pA 499 -30.37 -5.42 3.72e+01 1e15A 499 -30.26 -5.42 3.73e+01 1as8A 343 -31.13 -5.39 3.82e+01 2azaA 129 -26.85 -5.33 3.99e+01