% 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.YGR023W.t2k-100-30-dssp-ehl2 Host: farm19.cse.ucsc.edu Sun Mar 19 13:00:05 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR023W % --------------------------------------------------------------------- % 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 YGR023W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR023W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 552 nodes, 905.34 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(=1.5350) * Reverse)^tau(=0.7840))) % 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 1fjmA 330 -25.63 -11.96 6.17e-01 1jk7A 323 -24.97 -11.72 7.18e-01 1d0nA 729 -27.36 -11.41 8.76e-01 1u32A 293 -24.34 -11.25 9.76e-01 1xm7A 195 -22.76 -11.03 1.13e+00 1dxrH 258 -25.24 -10.79 1.32e+00 6prcH 258 -25.24 -10.79 1.32e+00 1prcH 259 -25.15 -10.47 1.62e+00 1wkrA 340 -32.60 -9.68 2.75e+00 1q40B 219 -23.84 -9.07 4.16e+00 1cx8B 639 -26.96 -9.01 4.32e+00 1eysH 259 -26.14 -8.98 4.41e+00 1cx8A 639 -26.95 -8.89 4.71e+00 1bqhG 129 -26.89 -8.79 5.02e+00 1f28A 297 -20.42 -8.59 5.77e+00 1rxdA 159 -22.24 -8.58 5.79e+00 1t5hX 504 -23.95 -8.58 5.81e+00 1zckA 154 -22.27 -8.48 6.22e+00 2pec 353 -26.88 -8.46 6.33e+00 1rmg 422 -31.44 -8.28 7.16e+00 1p8xA 344 -22.32 -8.15 7.84e+00 1air 353 -26.49 -8.14 7.87e+00 2bzlA 325 -22.97 -8.04 8.43e+00 1gqpA 221 -20.69 -7.83 9.81e+00 1x24A 180 -21.87 -7.82 9.89e+00 1o88A 353 -26.50 -7.78 1.01e+01 1e2tA 284 -21.37 -7.78 1.02e+01 1culA 217 -18.55 -7.73 1.05e+01 1khbA 625 -25.09 -7.69 1.08e+01 1pujA 282 -20.02 -7.67 1.10e+01 1azsA 220 -18.64 -7.61 1.14e+01 6prcL 273 -21.05 -7.59 1.16e+01 1k42A 168 -24.09 -7.54 1.20e+01 1cjtA 217 -18.75 -7.50 1.24e+01 1dxrL 273 -21.06 -7.48 1.25e+01 2madH 373 -28.02 -7.42 1.31e+01 1adqH 225 -28.81 -7.32 1.40e+01 1oboA 169 -19.41 -7.32 1.41e+01 1jcrB 437 -18.25 -7.31 1.41e+01 1de4C 640 -23.88 -7.30 1.43e+01 1tdtA 259 -24.01 -7.28 1.44e+01 1d8dB 437 -18.18 -7.27 1.45e+01 1fn8A 224 -31.14 -7.26 1.46e+01 1pq7A 224 -31.14 -7.26 1.46e+01 2asi 360 -27.76 -7.13 1.61e+01 1e1hA 287 -23.26 -7.06 1.69e+01 2d0oB 125 -18.99 -7.03 1.73e+01 1try 224 -30.81 -6.98 1.79e+01 1izlA 360 -20.64 -6.95 1.82e+01 1gotB 340 -31.05 -6.83 1.99e+01 1zpsA 138 -20.14 -6.79 2.05e+01 1tbgA 340 -31.49 -6.74 2.13e+01 1f0lA 535 -24.41 -6.74 2.13e+01 3tdt 274 -23.48 -6.73 2.14e+01 2bbkH 355 -25.48 -6.73 2.14e+01 1ot1A 686 -25.88 -6.64 2.28e+01 1ft1B 437 -17.53 -6.63 2.31e+01 1k5cA 335 -26.43 -6.62 2.32e+01 1o0uA 429 -18.15 -6.60 2.35e+01 1a0rB 340 -30.94 -6.53 2.48e+01 1rcf 169 -18.73 -6.51 2.53e+01 2tdt 274 -23.19 -6.48 2.58e+01 2rmpA 361 -27.38 -6.46 2.61e+01 1ollA 188 -23.07 -6.46 2.62e+01 1tn6B 437 -17.45 -6.45 2.63e+01 2b8nA 429 -17.73 -6.44 2.66e+01 1kgqA 274 -23.12 -6.41 2.70e+01 1cxlA 686 -25.63 -6.41 2.71e+01 1y8qB 640 -19.86 -6.40 2.72e+01 1ld8B 437 -17.34 -6.39 2.74e+01 1jfkA 134 -16.77 -6.37 2.79e+01 1m56B 264 -19.85 -6.34 2.85e+01 1tikA 213 -17.96 -6.28 2.98e+01 1zq1A 438 -21.57 -6.26 3.03e+01 1v54B 227 -22.97 -6.18 3.20e+01 1spuB 727 -23.32 -6.11 3.38e+01 1ah0 316 -17.78 -6.10 3.41e+01 1z3iX 644 -18.22 -6.10 3.41e+01 1jofA 365 -27.93 -6.08 3.46e+01 1xubA 298 -20.65 -6.00 3.67e+01 1oacA 727 -23.43 -5.99 3.70e+01 1svb 395 -20.42 -5.97 3.75e+01 1d6zA 727 -23.04 -5.97 3.75e+01 1yxmA 303 -16.57 -5.95 3.79e+01 1upiA 225 -26.42 -5.90 3.94e+01