% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YCL023C.t2k-100-30-dssp-ehl2 Host: cc66 Mon Nov 11 14:47:54 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YCL0/YCL023C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.dssps % % 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 YCL023C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YCL023C.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 116 nodes, 77.62 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(=2.5924) * Reverse)^tau(=0.7491))) % 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 1e4fT 419 -27.13 -6.15 2.56e+00 1bp7A 152 -24.55 -5.79 3.65e+00 1g9zA 152 -24.52 -5.74 3.82e+00 1af5 126 -23.51 -5.69 4.02e+00 1e8gA 560 -27.36 -5.56 4.57e+00 1qltA 560 -27.38 -5.55 4.60e+00 1lnrI 134 -24.28 -5.49 4.88e+00 1vaoA 560 -26.92 -5.29 5.95e+00 1dxrL 273 -26.88 -5.19 6.64e+00 6prcL 273 -26.88 -5.17 6.75e+00 1a27 289 -26.95 -4.80 9.88e+00 1fdt 327 -27.08 -4.79 9.97e+00 1lay 256 -25.29 -4.73 1.06e+01 1wpoB 256 -24.64 -4.70 1.09e+01 1gatA 60 -20.84 -4.64 1.17e+01 2gatA 66 -20.94 -4.53 1.30e+01 3gatA 66 -20.94 -4.53 1.30e+01 1c9oA 66 -20.60 -4.52 1.31e+01 1fd9A 213 -23.47 -4.45 1.41e+01 1lj2A 110 -22.87 -4.44 1.43e+01 1smpI 101 -21.30 -4.43 1.44e+01 1efnB 152 -22.89 -4.39 1.51e+01 1h95A 79 -21.19 -4.39 1.51e+01 2tysA 268 -23.89 -4.39 1.51e+01 1qopA 268 -23.84 -4.36 1.56e+01 1fds 327 -27.06 -4.27 1.71e+01 2wsyA 268 -23.85 -4.27 1.72e+01 1bksA 268 -23.84 -4.24 1.77e+01 1jb0A 755 -28.76 -4.21 1.83e+01 1jepA 222 -23.73 -4.05 2.17e+01 1aocA 175 -22.59 -4.04 2.19e+01 1eyqA 222 -23.73 -4.03 2.21e+01 1wpoA 256 -24.03 -4.02 2.24e+01 1eypA 222 -23.68 -4.01 2.25e+01 1bhdA 118 -21.65 -3.98 2.34e+01 1jjtA 228 -23.72 -3.94 2.45e+01 1ecsA 126 -21.62 -3.91 2.53e+01 1ewjA 126 -21.56 -3.87 2.63e+01 1dd6A 228 -23.58 -3.79 2.87e+01 1h9jA 145 -21.62 -3.79 2.87e+01 1h9mA 145 -21.61 -3.78 2.90e+01 1aoxA 203 -24.04 -3.78 2.91e+01 1fthA 122 -21.45 -3.71 3.14e+01 1qhuA 460 -25.26 -3.66 3.31e+01 1dc1A 323 -24.58 -3.63 3.41e+01 6gsvA 217 -23.08 -3.61 3.48e+01 1lylA 504 -25.63 -3.57 3.64e+01 1nbaA 264 -23.98 -3.51 3.92e+01 1lst 239 -22.76 -3.50 3.96e+01 1ttbA 127 -21.87 -3.49 3.99e+01