% 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.YGR025W.t2k-w0.5.mod Host: cc47 Fri Nov 8 17:35:35 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR025W % --------------------------------------------------------------------- % Inserted Files: YGR025W.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: YGR025W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 101 nodes, 99.80 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(=3.6429) * Reverse)^tau(=0.6990))) % 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 1khuA 218 -26.07 -7.05 4.66e-01 1fi8D 58 -22.52 -6.48 8.03e-01 1f2xL 135 -24.06 -6.40 8.67e-01 1ezuA 142 -24.56 -6.29 9.71e-01 1sluA 142 -24.42 -6.21 1.05e+00 1slvA 142 -24.42 -6.21 1.05e+00 1g6vK 126 -23.72 -6.17 1.10e+00 1ecy 142 -24.38 -6.12 1.15e+00 1qngA 170 -25.75 -6.11 1.16e+00 1id5I 142 -24.19 -6.11 1.17e+00 1f8tL 219 -25.05 -6.05 1.23e+00 1qnhA 170 -25.75 -6.04 1.25e+00 1yejL 219 -24.82 -6.00 1.30e+00 1yedA 219 -24.82 -5.98 1.32e+00 1yecL 219 -24.82 -5.97 1.33e+00 1ifgA 140 -24.12 -5.87 1.48e+00 1ezsA 142 -23.98 -5.87 1.48e+00 1eaiC 61 -23.23 -5.68 1.80e+00 2csn 297 -25.43 -5.04 3.49e+00 1csn 298 -25.44 -5.04 3.49e+00 1k0fA 277 -24.33 -4.98 3.71e+00 1toaA 313 -24.45 -4.88 4.14e+00 1am2 199 -23.17 -4.82 4.42e+00 1gkzA 388 -25.10 -4.82 4.43e+00 1gkxA 388 -25.10 -4.82 4.43e+00 1ddvA 111 -21.77 -4.40 6.98e+00 1yeeL 219 -23.18 -4.36 7.26e+00 1cld 61 -21.00 -4.36 7.27e+00 1irk 306 -24.54 -4.21 8.62e+00 1i44A 306 -24.54 -4.21 8.62e+00 1ir3A 306 -24.54 -4.20 8.71e+00 1h70A 255 -23.07 -4.13 9.40e+00 1dsfL 112 -21.65 -4.09 9.86e+00 1mak 113 -21.23 -4.09 9.87e+00 1i2hA 168 -22.19 -4.08 1.00e+01 1dfnA 30 -19.30 -4.07 1.00e+01 1jj2I 145 -21.85 -3.95 1.16e+01 1ffkG 145 -21.85 -3.95 1.16e+01 1jfkA 134 -21.49 -3.89 1.24e+01 1kz7A 353 -24.29 -3.88 1.25e+01 1bjqB 253 -23.04 -3.86 1.28e+01 1eot 74 -20.35 -3.85 1.30e+01 1ddwA 120 -21.32 -3.82 1.33e+01 1iehA 135 -21.13 -3.81 1.35e+01 1fu1B 203 -22.48 -3.81 1.35e+01 1fu1A 203 -22.48 -3.81 1.35e+01 1bkdS 439 -24.85 -3.74 1.48e+01 1i7aA 111 -21.00 -3.70 1.55e+01 1qhxA 178 -21.83 -3.69 1.57e+01 1qhsA 178 -21.83 -3.69 1.57e+01 1qhnA 178 -21.91 -3.65 1.64e+01 1apyB 141 -21.34 -3.60 1.73e+01 1lb1A 353 -24.01 -3.47 2.03e+01 1cy7A 599 -24.57 -3.44 2.09e+01 1ecl 597 -24.57 -3.43 2.11e+01 1kzgA 353 -24.01 -3.42 2.13e+01 1df0A 700 -25.12 -3.38 2.25e+01 1il1B 219 -22.17 -3.34 2.37e+01 1ddzA 496 -23.79 -3.24 2.64e+01 1g10A 102 -20.77 -3.24 2.66e+01 1dlfL 113 -20.36 -3.22 2.73e+01 1bj7 156 -21.68 -3.16 2.91e+01 1lo4L 217 -22.22 -3.16 2.94e+01 1pvaA 110 -19.99 -3.14 3.00e+01 1fptL 219 -22.22 -3.14 3.00e+01 1c1zA 326 -25.02 -3.10 3.17e+01 1a1z 91 -19.44 -3.10 3.17e+01 1qubA 319 -25.00 -3.09 3.20e+01 1j4eA 363 -22.69 -3.06 3.32e+01 1je5A 206 -21.63 -3.05 3.33e+01 1nldL 219 -22.11 -3.05 3.35e+01 1d2oA 187 -21.43 -3.03 3.41e+01 1gk8I 140 -21.40 -3.02 3.47e+01 1d2pA 373 -22.80 -2.99 3.60e+01 1nra 63 -19.32 -2.96 3.74e+01 1a1w 91 -19.44 -2.95 3.80e+01 1mnuL 219 -21.93 -2.95 3.81e+01 1k77A 260 -22.03 -2.94 3.84e+01 1jh5A 144 -20.82 -2.92 3.93e+01