% 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.YCL021W-A.t2k-w0.5.mod Host: cc49 Thu Oct 31 21:16:09 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YCL0/YCL021W-A % --------------------------------------------------------------------- % Inserted Files: YCL021W-A.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: YCL021W-A.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 126 nodes, 124.48 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(=4.1303) * Reverse)^tau(=0.6290))) % 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 1kf6D 119 -28.29 -9.85 2.48e-01 1i3uA 127 -24.25 -6.72 2.24e+00 1i3vA 129 -24.26 -6.70 2.27e+00 1i35A 95 -22.90 -5.66 5.13e+00 1ck7A 631 -27.13 -5.64 5.22e+00 1k8rB 110 -23.05 -5.42 6.26e+00 1i82A 189 -24.03 -5.34 6.69e+00 1i8aA 189 -24.03 -5.34 6.69e+00 1yagA 375 -25.68 -5.21 7.41e+00 1yvnA 375 -25.68 -5.20 7.51e+00 1jx7A 117 -23.26 -4.84 1.02e+01 1dejA 375 -24.98 -4.69 1.15e+01 1dgaA 375 -24.97 -4.69 1.15e+01 1c0fA 368 -24.95 -4.69 1.16e+01 1c0gA 375 -24.98 -4.68 1.16e+01 1b5eA 246 -24.03 -4.63 1.22e+01 1yuhB 218 -24.26 -4.61 1.23e+01 1ilvB 247 -24.34 -4.47 1.40e+01 1jm7B 117 -22.42 -4.44 1.43e+01 1itvA 195 -24.43 -4.29 1.63e+01 1atnA 373 -24.61 -4.27 1.67e+01 1lcuB 371 -24.61 -4.27 1.67e+01 1db0A 371 -24.61 -4.26 1.68e+01 1j6zA 376 -24.62 -4.26 1.68e+01 1kxpA 375 -24.62 -4.26 1.68e+01 1eqyA 377 -24.62 -4.26 1.68e+01 1ijjB 377 -24.62 -4.26 1.68e+01 1j9lA 247 -24.17 -4.22 1.74e+01 1j9jA 247 -24.17 -4.22 1.74e+01 1cc1S 283 -24.88 -4.18 1.82e+01 1bmv2 374 -24.47 -4.16 1.85e+01 1k4cA 219 -22.90 -4.01 2.10e+01 1m2oA 768 -26.06 -3.98 2.17e+01 1d9uA 154 -22.50 -3.95 2.23e+01 1ho8A 480 -24.96 -3.90 2.34e+01 1lk0A 131 -22.06 -3.90 2.34e+01 1a38P 20 -17.29 -3.88 2.37e+01 1g25A 65 -21.13 -3.86 2.43e+01 1pdkA 218 -23.31 -3.84 2.46e+01 1qppA 218 -23.31 -3.84 2.48e+01 3dpa 218 -23.31 -3.83 2.48e+01 1gpc 218 -23.00 -3.79 2.58e+01 1d4xA 375 -24.76 -3.74 2.71e+01 1eo8H 217 -22.62 -3.64 2.98e+01 1cczA 171 -23.20 -3.55 3.25e+01 1qa9B 95 -21.22 -3.53 3.31e+01 1tfd 304 -23.30 -3.52 3.34e+01 1afvH 220 -22.49 -3.47 3.49e+01 1ceo 343 -24.31 -3.47 3.50e+01 1cec 343 -24.30 -3.46 3.53e+01 1esc 306 -23.31 -3.46 3.54e+01 1fi4A 416 -24.92 -3.44 3.59e+01 2dln 306 -23.49 -3.43 3.64e+01 1i7iA 292 -22.90 -3.37 3.87e+01 1jj2S 119 -21.98 -3.36 3.90e+01 1ffkQ 119 -21.98 -3.36 3.90e+01