% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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-T2K, 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, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % stridefoo.1.YDR524W-C.t2k-100-30-stride-ebghtl Host: farm16.cse.ucsc.edu Fri Mar 3 08:01:55 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDR5/YDR524W-C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YDR524W-C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDR524W-C.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14381 sequences, 3373755 residues, 30 nodes, 51.90 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 (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=5.7457) * Reverse)^tau(=0.6868))) % Calculated when Simple < simple_threshold (10000.00) % 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 1vqsA 116 -11.43 -5.50 2.44e-01 2a9uA 144 -10.56 -4.58 8.63e-01 1ebmA 317 -10.79 -4.33 1.24e+00 1m3qA 317 -10.79 -4.32 1.25e+00 1lwyA 324 -10.76 -4.30 1.28e+00 1ko9A 345 -10.71 -4.24 1.42e+00 1fvpA 231 -11.66 -4.24 1.42e+00 1aijS 301 -10.46 -4.05 1.87e+00 1aijM 307 -10.44 -4.04 1.90e+00 1rzhM 307 -10.44 -4.01 1.96e+00 1vmhA 144 -9.56 -3.79 2.76e+00 1qwoA 442 -10.28 -3.68 3.25e+00 1qyp 57 -9.12 -3.67 3.28e+00 1ax0 239 -9.57 -3.52 4.16e+00 1h8eD 482 -9.72 -3.42 4.80e+00 1e5rA 290 -9.48 -3.41 4.90e+00 1e79D 482 -9.72 -3.37 5.22e+00 1gzcA 239 -9.39 -3.29 5.87e+00 1nwaA 203 -9.52 -3.26 6.20e+00 1xbfA 140 -8.98 -3.25 6.29e+00 1mk4A 157 -9.05 -2.88 1.14e+01 1dusA 194 -8.48 -2.85 1.20e+01 1f9zA 135 -9.01 -2.84 1.22e+01 1y8cA 246 -8.79 -2.81 1.28e+01 1fa8A 135 -9.01 -2.80 1.30e+01 1eq3A 96 -8.95 -2.78 1.34e+01 1euiA 228 -9.32 -2.78 1.34e+01 1j5jA 36 -8.68 -2.68 1.57e+01 1pu5A 164 -8.63 -2.67 1.61e+01 1flzA 228 -9.21 -2.67 1.62e+01 1qcxA 359 -8.41 -2.66 1.64e+01 2fhpA 187 -8.50 -2.66 1.65e+01 1wd6A 123 -9.42 -2.64 1.70e+01 1q4uA 151 -8.47 -2.62 1.75e+01 1g13A 162 -8.52 -2.60 1.83e+01 1imoA 88 -8.44 -2.57 1.90e+01 4eugA 229 -9.24 -2.55 1.98e+01 1svr 114 -8.55 -2.50 2.15e+01 1eugA 229 -9.12 -2.49 2.21e+01 3eugA 229 -9.14 -2.47 2.25e+01 1xmpA 170 -8.57 -2.44 2.40e+01 1e85A 127 -8.14 -2.44 2.40e+01 1b73A 254 -8.43 -2.41 2.53e+01 1vmfA 145 -7.91 -2.36 2.74e+01 2mev1 277 -8.48 -2.35 2.80e+01 1b74A 254 -8.44 -2.35 2.80e+01 1q87A 221 -8.44 -2.33 2.90e+01 1v9sA 208 -8.20 -2.32 2.94e+01 2ag4A 164 -8.23 -2.28 3.14e+01 1ty9A 222 -8.17 -2.28 3.16e+01 1j9jA 247 -8.29 -2.22 3.47e+01 1wxxA 382 -8.72 -2.22 3.47e+01 1qwdA 177 -8.03 -2.22 3.48e+01 1j9lA 247 -8.29 -2.22 3.52e+01 1vm8A 534 -8.86 -2.21 3.54e+01 1ufwA 95 -8.08 -2.20 3.62e+01 1hv2A 99 -7.90 -2.16 3.87e+01 1dbtA 239 -8.23 -2.15 3.98e+01