% 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.YAL028W.t2k-100-30-str Host: cc66 Sun Nov 10 21:39:29 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YAL0/YAL028W % --------------------------------------------------------------------- % 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 YAL028W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YAL028W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 529 nodes, 360.35 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(=1.3251) * Reverse)^tau(=0.7978))) % 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 1jchA 551 -57.65 -16.73 5.24e-02 1jchC 551 -57.65 -16.73 5.24e-02 1h3nA 878 -43.82 -12.98 4.59e-01 1llp 343 -41.30 -11.01 1.51e+00 1cii 602 -55.00 -10.49 2.09e+00 1gylA 369 -34.98 -10.18 2.52e+00 7catA 506 -37.29 -10.16 2.56e+00 1gm7A 209 -36.55 -9.60 3.63e+00 1epwA 1290 -49.65 -9.58 3.69e+00 1li5A 461 -40.03 -9.52 3.83e+00 1dmr 823 -36.24 -9.26 4.51e+00 1ddbA 195 -34.72 -9.16 4.79e+00 1jwgA 147 -37.08 -8.82 5.97e+00 1dgfA 497 -34.76 -8.71 6.43e+00 1rmi 160 -37.30 -8.69 6.50e+00 1fzaB 328 -34.61 -8.57 7.01e+00 1ai7A 209 -36.36 -8.55 7.11e+00 1ajqA 209 -37.32 -8.55 7.11e+00 1eo9A 209 -31.97 -8.53 7.20e+00 1ju2A 536 -35.87 -8.41 7.81e+00 1i6lA 328 -36.68 -8.40 7.85e+00 1bk0 331 -32.01 -8.38 7.94e+00 1i6kA 328 -36.61 -8.33 8.19e+00 1j5wA 298 -36.61 -8.31 8.29e+00 1dc1A 323 -37.43 -8.23 8.73e+00 1d2rB 326 -36.32 -8.22 8.81e+00 1d2rA 326 -36.29 -8.19 8.98e+00 1dghB 498 -34.19 -8.14 9.28e+00 1hu3A 260 -41.62 -8.11 9.48e+00 1d0yA 761 -35.09 -8.09 9.56e+00 1fftC 204 -33.92 -8.04 9.93e+00 5csmA 256 -37.11 -8.02 1.01e+01 1pnkA 209 -35.55 -8.00 1.01e+01 8kme2 259 -30.88 -8.00 1.02e+01 1h8dH 260 -31.04 -7.92 1.08e+01 1c5lH 259 -30.86 -7.78 1.18e+01 1m55A 197 -30.65 -7.66 1.28e+01 1qfoC 119 -28.28 -7.64 1.29e+01 1cojA 212 -34.98 -7.60 1.33e+01 1g2nA 264 -35.51 -7.59 1.34e+01 1gk9A 260 -37.22 -7.55 1.37e+01 1qfoA 119 -27.82 -7.46 1.45e+01 1jr3A 373 -33.84 -7.43 1.48e+01 1vpfA 102 -26.09 -7.42 1.49e+01 1ahtH 259 -30.62 -7.37 1.54e+01 1e3aA 260 -37.57 -7.27 1.64e+01 1ll0A 339 -30.15 -7.19 1.73e+01 1ihgA 370 -43.34 -7.12 1.82e+01 1ll2A 333 -30.38 -7.12 1.82e+01 1qoyA 318 -45.82 -7.09 1.86e+01 1ubpC 570 -31.46 -6.96 2.02e+01 1iab 200 -33.18 -6.94 2.06e+01 1eyeA 280 -28.80 -6.85 2.19e+01 1lvk 762 -34.03 -6.82 2.23e+01 1au1A 166 -36.44 -6.79 2.28e+01 1qkmA 255 -37.77 -6.72 2.38e+01 1fa0A 537 -33.57 -6.71 2.41e+01 1vom 762 -33.18 -6.66 2.49e+01 1fa0B 537 -33.36 -6.61 2.57e+01 1wer 334 -36.90 -6.60 2.58e+01 1cf9A 753 -34.55 -6.58 2.63e+01 2bidA 197 -32.90 -6.57 2.64e+01 1ifa 158 -30.96 -6.56 2.65e+01 1a7j 290 -30.99 -6.52 2.74e+01 1l8yA 91 -30.73 -6.44 2.88e+01 1fltV 98 -24.83 -6.41 2.93e+01 1eu1A 780 -33.53 -6.38 3.01e+01 2occD 147 -28.87 -6.38 3.02e+01 1ocrD 147 -28.87 -6.37 3.03e+01 1vaoA 560 -35.64 -6.37 3.03e+01 1sig 339 -40.90 -6.35 3.07e+01 1e55A 512 -30.78 -6.26 3.27e+01 1eyvA 156 -30.40 -6.21 3.38e+01 1dszA 86 -27.14 -6.21 3.39e+01 1a41 234 -32.73 -6.20 3.40e+01 2bce 581 -31.19 -6.18 3.46e+01 1colA 204 -35.58 -6.17 3.46e+01 4ubpC 570 -30.67 -6.16 3.48e+01 1e7lA 157 -29.55 -6.14 3.54e+01 1nfa 178 -31.33 -6.13 3.57e+01 1c7qA 445 -30.70 -6.06 3.74e+01 1m7sA 484 -36.65 -6.05 3.76e+01 1a6dA 545 -33.74 -6.05 3.77e+01 1i0aA 466 -38.24 -6.03 3.81e+01 1jpmA 366 -30.00 -6.01 3.87e+01 1gakA 141 -35.35 -6.01 3.87e+01 1en7A 157 -28.54 -5.99 3.94e+01