% 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. % --------------------------------------------------------------------- % str2foo.1.YDL045W-A.t2k-100-30-str2 Host: farm13 Mon Nov 29 12:11:32 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDL0/YDL045W-A % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s % % 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 YDL045W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDL045W-A.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 96 nodes, 105.02 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(=2.0526) * Reverse)^tau(=0.7396))) % 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 1u96A 69 -23.28 -12.89 1.36e-01 1r0pA 312 -21.41 -11.19 4.17e-01 1qhfA 240 -19.27 -10.83 5.30e-01 2hp8 68 -25.59 -10.58 6.27e-01 1bq3B 246 -18.74 -10.24 7.91e-01 1hp8 68 -25.33 -10.01 9.28e-01 1fadA 99 -19.76 -9.40 1.42e+00 1unlD 208 -22.09 -9.23 1.60e+00 1pb6A 212 -18.55 -8.31 3.10e+00 1fvrA 327 -19.65 -8.15 3.46e+00 1e3yA 104 -19.60 -8.09 3.62e+00 1ehyA 294 -17.35 -8.01 3.84e+00 3pgm 241 -17.01 -7.91 4.14e+00 1jpaA 312 -19.80 -7.71 4.81e+00 1m4uA 206 -17.37 -7.66 4.97e+00 1n8vA 112 -19.56 -7.46 5.76e+00 1lj8A 493 -17.05 -7.36 6.23e+00 1je8A 82 -16.88 -7.31 6.48e+00 1hz4A 373 -18.39 -7.24 6.81e+00 1qqiA 104 -15.74 -7.09 7.62e+00 1fgkA 310 -18.06 -7.04 7.94e+00 1pfvA 551 -17.04 -6.94 8.51e+00 1opjA 293 -17.74 -6.94 8.54e+00 1f4lA 551 -17.03 -6.94 8.57e+00 1u46A 291 -17.26 -6.93 8.60e+00 1kx9A 112 -19.33 -6.83 9.27e+00 1u59A 287 -17.75 -6.80 9.46e+00 1irk 306 -18.03 -6.71 1.02e+01 1jwgA 147 -18.19 -6.71 1.02e+01 1ujkA 147 -18.19 -6.71 1.02e+01 1qqtA 551 -16.73 -6.67 1.05e+01 1xbbA 291 -16.49 -6.54 1.16e+01 1ir3A 306 -17.81 -6.54 1.16e+01 1mdoA 393 -15.98 -6.37 1.32e+01 1rijA 25 -15.43 -6.22 1.49e+01 1wndA 495 -15.39 -6.16 1.55e+01 1w7bA 339 -17.04 -6.14 1.58e+01 1ir6A 424 -16.42 -6.11 1.61e+01 1gxqA 106 -14.98 -6.04 1.71e+01 1mw7A 240 -14.96 -6.03 1.73e+01 1axn 323 -17.42 -5.91 1.89e+01 1fhjB 146 -16.02 -5.90 1.92e+01 1hulA 108 -16.49 -5.88 1.94e+01 1i4yA 114 -16.70 -5.85 1.98e+01 1u84A 90 -18.09 -5.84 2.00e+01 1qpcA 279 -15.99 -5.77 2.12e+01 1a41 234 -15.78 -5.75 2.16e+01 1babB 146 -16.12 -5.73 2.19e+01 1dxtB 147 -16.12 -5.73 2.19e+01 1ddf 127 -15.69 -5.71 2.23e+01 1p4oA 322 -17.91 -5.70 2.23e+01 1mn1 357 -14.98 -5.70 2.24e+01 1howA 373 -15.40 -5.70 2.25e+01 1h4lD 147 -18.51 -5.70 2.25e+01 1irdB 146 -15.81 -5.69 2.25e+01 1g0dA 695 -14.28 -5.69 2.26e+01 1h2vC 771 -17.84 -5.68 2.28e+01 1j7yB 146 -15.92 -5.62 2.39e+01 1ax4A 467 -14.93 -5.56 2.51e+01 1e79A 510 -14.25 -5.54 2.54e+01 1syyA 346 -16.67 -5.50 2.64e+01 1iufA 144 -16.62 -5.49 2.66e+01 1mp8A 281 -15.35 -5.47 2.70e+01 1i88A 389 -14.90 -5.47 2.70e+01 1bi5A 389 -14.91 -5.46 2.71e+01 1i86A 389 -14.91 -5.46 2.71e+01 1j5vA 351 -13.95 -5.46 2.72e+01 1kngA 156 -14.66 -5.45 2.73e+01 1v2dA 381 -14.45 -5.45 2.74e+01 1mldA 314 -14.71 -5.41 2.83e+01 1k77A 260 -13.82 -5.39 2.87e+01 1qlaB 239 -14.17 -5.37 2.93e+01 1g87A 614 -15.54 -5.36 2.96e+01 1hyuA 521 -14.43 -5.35 2.97e+01 1dguA 183 -18.75 -5.35 2.98e+01 1htyA 1015 -14.51 -5.32 3.04e+01 1hxkA 1015 -14.51 -5.32 3.05e+01 1dk8A 147 -16.77 -5.31 3.06e+01 1hwwA 1015 -14.50 -5.31 3.07e+01 1ji8A 111 -14.16 -5.31 3.07e+01 1i12A 160 -15.57 -5.31 3.08e+01 1avc 673 -18.23 -5.30 3.09e+01 1a26 361 -15.54 -5.28 3.13e+01 1nogA 177 -17.13 -5.28 3.15e+01 1fmk 452 -16.47 -5.27 3.17e+01 1dl5A 317 -13.45 -5.27 3.18e+01 1qwnA 1045 -14.50 -5.26 3.19e+01 1cqxA 403 -17.07 -5.26 3.20e+01 1crl 534 -15.29 -5.24 3.24e+01 1f8aB 167 -15.34 -5.24 3.25e+01 1i1dA 161 -15.06 -5.23 3.26e+01 1zug 71 -13.55 -5.18 3.40e+01 1a04A 215 -16.18 -5.18 3.40e+01 1h6kA 757 -17.69 -5.17 3.45e+01 1oi2A 366 -15.07 -5.16 3.46e+01 1q8yA 373 -15.73 -5.15 3.50e+01 1tafA 68 -14.66 -5.12 3.60e+01 1po5A 476 -15.91 -5.11 3.62e+01 1puoA 170 -15.46 -5.11 3.62e+01 1g60A 260 -13.92 -5.09 3.66e+01 1fjgB 256 -14.08 -5.09 3.68e+01 1ck7A 631 -14.55 -5.05 3.81e+01 1xxbA 78 -13.07 -5.04 3.83e+01 1gg3A 279 -15.30 -5.04 3.83e+01 1cleA 534 -15.24 -5.03 3.85e+01 1ivhA 394 -16.44 -5.03 3.85e+01 1onrA 316 -14.67 -5.02 3.90e+01 1h6oA 204 -16.19 -5.00 3.95e+01 1jb0F 164 -16.13 -4.99 3.98e+01