% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YDR524W-C.t2k-100-30-dssp-ehl2 Host: farm16.cse.ucsc.edu Fri Mar 3 08:06:14 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.dssps % % 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.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14381 sequences, 3373755 residues, 30 nodes, 51.81 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(=5.8380) * Reverse)^tau(=0.6832))) % 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 -11.75 -5.67 1.98e-01 1e5rA 290 -10.76 -4.53 9.33e-01 1aijS 301 -10.64 -4.37 1.17e+00 1aijM 307 -10.62 -4.36 1.20e+00 1rzhM 307 -10.62 -4.36 1.20e+00 1vmhA 144 -10.32 -4.26 1.37e+00 1xbfA 140 -10.18 -4.15 1.62e+00 2a9uA 144 -9.87 -4.10 1.73e+00 1fvpA 231 -10.96 -3.90 2.33e+00 1ebmA 317 -10.22 -3.71 3.08e+00 1lwyA 324 -10.20 -3.69 3.18e+00 1m3qA 317 -10.21 -3.67 3.28e+00 1qyp 57 -9.48 -3.64 3.45e+00 1ko9A 345 -10.14 -3.63 3.50e+00 1e79D 482 -10.03 -3.57 3.85e+00 1h8eD 482 -10.03 -3.55 3.96e+00 1vmfA 145 -9.39 -3.55 3.96e+00 2a8eA 220 -9.55 -3.37 5.19e+00 1ax0 239 -9.55 -3.22 6.58e+00 1qwoA 442 -9.69 -3.13 7.62e+00 1mk4A 157 -9.39 -2.97 9.78e+00 1gzcA 239 -9.39 -2.97 9.83e+00 1f9zA 135 -9.18 -2.94 1.04e+01 1fa8A 135 -9.18 -2.93 1.04e+01 2agcA 162 -9.10 -2.92 1.06e+01 1q4uA 151 -8.82 -2.86 1.17e+01 1wd6A 123 -9.75 -2.78 1.34e+01 1qwdA 177 -8.81 -2.74 1.43e+01 2fj8A 125 -8.58 -2.69 1.55e+01 1gr0A 367 -8.75 -2.63 1.72e+01 1eq3A 96 -8.97 -2.63 1.72e+01 2ag4A 164 -8.81 -2.61 1.76e+01 1pu5A 164 -8.80 -2.61 1.79e+01 1m4lA 307 -9.04 -2.60 1.80e+01 1y8cA 246 -8.75 -2.60 1.80e+01 6cpa 307 -9.04 -2.60 1.81e+01 1bavA 309 -9.04 -2.59 1.82e+01 2ctc 307 -9.04 -2.58 1.85e+01 1yme 309 -9.04 -2.58 1.85e+01 2ctb 307 -9.04 -2.58 1.86e+01 1g13A 162 -8.80 -2.58 1.86e+01 2ag9A 164 -8.99 -2.53 2.04e+01 1nwaA 203 -9.02 -2.51 2.10e+01 1cgo 127 -8.13 -2.51 2.11e+01 1i8jA 323 -9.24 -2.50 2.12e+01 1l6sA 323 -9.24 -2.50 2.14e+01 1c2aA 120 -8.33 -2.46 2.30e+01 1e85A 127 -8.06 -2.44 2.38e+01 1b4eA 323 -9.24 -2.43 2.41e+01 1molA 94 -8.30 -2.38 2.63e+01 1v9sA 208 -8.36 -2.35 2.77e+01 1v0dA 329 -8.98 -2.32 2.91e+01 2fhpA 187 -8.20 -2.28 3.11e+01 1dmlA 319 -9.19 -2.27 3.15e+01 2mev1 277 -8.69 -2.27 3.17e+01 1j9jA 247 -8.47 -2.25 3.29e+01 1j9lA 247 -8.47 -2.25 3.29e+01 1ty9A 222 -8.22 -2.23 3.41e+01 1ic9A 29 -7.86 -2.23 3.42e+01 1wxxA 382 -8.99 -2.23 3.42e+01 1svq 114 -8.34 -2.22 3.44e+01 1tetH 210 -8.76 -2.22 3.46e+01 1ci3M 249 -8.27 -2.21 3.53e+01 1flzA 228 -9.01 -2.21 3.54e+01 1ufwA 95 -8.11 -2.20 3.57e+01 4eugA 229 -8.92 -2.14 3.99e+01 1eugA 229 -8.92 -2.14 4.00e+01