% 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.YGR035C.t2k-w0.5.mod Host: cc41 Fri Nov 8 18:50:19 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR035C % --------------------------------------------------------------------- % Inserted Files: YGR035C.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: YGR035C.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 117 nodes, 115.24 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(=3.3646) * Reverse)^tau(=0.7069))) % 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 1lba 146 -25.95 -7.41 4.40e-01 1aroL 151 -25.98 -7.35 4.70e-01 1a3gA 308 -25.55 -5.99 1.71e+00 1i1kA 309 -25.55 -5.99 1.72e+00 1c17M 177 -24.79 -5.45 2.95e+00 1j79A 347 -25.14 -5.24 3.66e+00 1g10A 102 -21.78 -4.72 6.26e+00 1ig9A 903 -26.97 -4.53 7.67e+00 1clqA 903 -26.97 -4.53 7.70e+00 1e9kA 38 -19.07 -4.46 8.31e+00 1c07A 95 -21.52 -4.33 9.53e+00 1jyoA 130 -22.04 -4.21 1.09e+01 1kqfC 217 -24.33 -4.20 1.10e+01 1gtzA 156 -23.07 -4.15 1.15e+01 1d0iA 156 -23.05 -4.13 1.18e+01 1loqA 228 -23.17 -4.11 1.21e+01 1nqbA 256 -23.42 -3.94 1.47e+01 1km6A 247 -23.17 -3.92 1.49e+01 1klyA 247 -23.07 -3.92 1.49e+01 1km4A 247 -23.16 -3.87 1.57e+01 1losA 224 -22.88 -3.85 1.62e+01 1dv7A 227 -22.89 -3.85 1.62e+01 1lorA 228 -22.90 -3.84 1.64e+01 1lolA 229 -22.90 -3.83 1.66e+01 1klzA 247 -22.98 -3.83 1.66e+01 1im8A 244 -23.33 -3.79 1.72e+01 1be3I 78 -20.75 -3.76 1.79e+01 1k5dB 201 -23.23 -3.74 1.82e+01 1rmd 116 -21.84 -3.73 1.84e+01 1km1A 247 -23.04 -3.72 1.87e+01 1dhs 344 -23.85 -3.70 1.91e+01 1km0A 247 -22.95 -3.69 1.92e+01 1ggvA 232 -22.74 -3.69 1.93e+01 1bv8A 138 -22.10 -3.69 1.94e+01 1dvjA 246 -22.97 -3.66 2.00e+01 1dvjC 246 -22.97 -3.66 2.00e+01 1km2A 247 -22.97 -3.65 2.01e+01 1km3A 247 -22.97 -3.65 2.03e+01 1km5A 247 -22.89 -3.57 2.21e+01 1din 234 -22.70 -3.56 2.23e+01 1mma 762 -25.43 -3.48 2.46e+01 1fmvA 761 -25.42 -3.46 2.51e+01 1d0yA 761 -25.41 -3.46 2.52e+01 1jwyA 776 -25.44 -3.46 2.52e+01 1qlaB 239 -22.71 -3.45 2.53e+01 1hllA 32 -17.81 -3.45 2.54e+01 1bn7A 294 -23.06 -3.41 2.65e+01 1bn6A 294 -23.06 -3.41 2.65e+01 1cqwA 295 -23.06 -3.40 2.70e+01 1ykfA 352 -23.71 -3.37 2.78e+01 1ho9A 32 -18.04 -3.36 2.82e+01 1qe3A 489 -23.93 -3.30 3.01e+01 1cbkA 160 -22.56 -3.23 3.28e+01 1em9A 154 -21.36 -3.23 3.30e+01 1fvpA 231 -22.38 -3.18 3.47e+01 1c7iA 489 -24.07 -3.16 3.58e+01 1vom 762 -25.11 -3.14 3.65e+01 1mnd 762 -25.11 -3.14 3.65e+01