% 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. % --------------------------------------------------------------------- % w0.5foo.1.YGR030C.t2k-w0.5.mod Host: cc50 Fri Nov 8 18:27:02 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR030C % --------------------------------------------------------------------- % Inserted Files: YGR030C.t2k-w0.5.mod % Database Files: /projects/compbio/experiments/protein-predict/SAM_T02/data/pdbaa % % 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)) % Single Track Model: YGR030C.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 159 nodes, 157.74 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(=2.6703) * Reverse)^tau(=0.7341))) % 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 1gm1A 94 -24.57 -7.09 1.27e+00 1qfoA 119 -24.85 -6.34 2.49e+00 1qfoC 119 -24.85 -6.34 2.49e+00 1d5gA 96 -23.53 -6.00 3.43e+00 1e7pA 656 -29.20 -5.95 3.61e+00 1e7pG 655 -29.20 -5.95 3.61e+00 1rblA 467 -27.36 -5.74 4.39e+00 1rscA 472 -27.37 -5.73 4.41e+00 1kbvA 327 -26.23 -5.70 4.58e+00 1ig8A 486 -27.95 -5.62 4.93e+00 3rubL 477 -27.06 -5.58 5.09e+00 1gvhA 396 -25.96 -5.49 5.56e+00 1rldA 446 -26.77 -5.46 5.72e+00 1gk8A 475 -27.30 -5.44 5.86e+00 1qlaA 656 -28.90 -5.43 5.92e+00 4rubA 477 -26.84 -5.43 5.93e+00 1ej7L 475 -26.83 -5.43 5.93e+00 1mldA 314 -26.19 -5.26 6.93e+00 1preB 470 -28.10 -5.24 7.12e+00 1preA 470 -28.10 -5.24 7.12e+00 1eo6A 117 -23.07 -5.23 7.19e+00 1fm0E 150 -23.86 -5.18 7.55e+00 1fmaE 150 -23.86 -5.18 7.55e+00 1hx1A 400 -26.67 -5.17 7.62e+00 1f59A 442 -26.01 -5.06 8.48e+00 1ibrB 462 -26.05 -5.02 8.77e+00 1gcjA 460 -25.83 -4.64 1.28e+01 1guhA 221 -25.01 -4.64 1.28e+01 1gseA 221 -25.00 -4.64 1.28e+01 1gw0A 559 -26.68 -4.61 1.33e+01 3gpdG 334 -24.96 -4.49 1.49e+01 1bla 155 -23.37 -4.46 1.54e+01 1bfc 147 -23.25 -4.44 1.56e+01 1bfg 146 -23.23 -4.44 1.57e+01 1iilA 155 -23.37 -4.44 1.57e+01 1bas 154 -23.36 -4.44 1.57e+01 1iunA 282 -24.42 -4.35 1.71e+01 2fgf 146 -23.23 -4.24 1.93e+01 4fgf 146 -23.23 -4.24 1.93e+01 1nsa 395 -25.11 -4.23 1.94e+01 1bupA 386 -25.67 -4.21 1.99e+01 1eysL 280 -24.07 -4.18 2.05e+01 1qgrA 876 -26.69 -4.16 2.09e+01 1rfnA 235 -23.53 -4.04 2.36e+01 1dawA 327 -24.90 -4.02 2.42e+01 1lpuA 332 -24.91 -4.01 2.44e+01 6prcL 273 -24.81 -4.00 2.47e+01 1dxrL 273 -24.81 -3.99 2.48e+01 7ca2 260 -24.05 -3.96 2.57e+01 1j71A 334 -24.87 -3.94 2.62e+01 1agsA 221 -23.83 -3.93 2.64e+01 1hjoA 380 -24.96 -3.92 2.69e+01 2tryA 127 -21.87 -3.86 2.86e+01 1fnyA 237 -24.17 -3.77 3.13e+01 1fs2A 272 -24.20 -3.66 3.53e+01 1uteA 313 -24.02 -3.65 3.55e+01 1b74A 254 -23.82 -3.64 3.59e+01 1b73A 254 -23.82 -3.64 3.59e+01 1fcqA 350 -24.66 -3.63 3.64e+01 1ko7A 314 -25.92 -3.63 3.65e+01 1bc9 200 -23.50 -3.60 3.74e+01 1f7cA 231 -23.28 -3.60 3.76e+01 1rxoB 475 -24.96 -3.59 3.79e+01 8rucA 475 -24.96 -3.59 3.80e+01 1nulA 152 -22.51 -3.58 3.86e+01 1eljA 381 -26.20 -3.57 3.86e+01 1gt7A 274 -23.63 -3.56 3.91e+01 1couA 85 -21.11 -3.55 3.95e+01