% 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.YGR035W-A.t2k-100-30-dssp-ehl2 Host: farm09.cse.ucsc.edu Sun Feb 12 22:09:04 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR035W-A % --------------------------------------------------------------------- % 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 YGR035W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR035W-A.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13614 sequences, 3208521 residues, 74 nodes, 117.44 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(=2.5469) * Reverse)^tau(=0.7696))) % 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 1zaaC 87 -17.96 -10.27 4.89e-02 1aayA 90 -17.93 -10.24 5.00e-02 1a1iA 90 -17.34 -9.65 8.64e-02 1g2fC 90 -16.69 -8.84 1.86e-01 1llmC 88 -14.54 -7.31 8.33e-01 2ashA 381 -15.14 -6.66 1.60e+00 1jnrB 150 -15.61 -6.60 1.70e+00 1tc5A 194 -14.15 -5.96 3.31e+00 1wthD 391 -14.16 -5.95 3.35e+00 1tqnA 486 -14.27 -5.79 3.96e+00 1xaoA 121 -13.85 -5.78 4.01e+00 1qlaB 239 -14.34 -5.61 4.75e+00 1xxsA 122 -14.46 -5.59 4.88e+00 1zcjA 463 -14.04 -5.55 5.10e+00 2aw4Z 70 -14.21 -5.52 5.26e+00 1s48A 609 -13.47 -5.51 5.31e+00 1uyjA 296 -13.73 -5.38 6.09e+00 1plfA 72 -13.24 -5.36 6.26e+00 1a0hA 159 -14.33 -5.31 6.61e+00 1hn6A 110 -14.64 -5.20 7.43e+00 1m3sA 186 -13.03 -5.17 7.63e+00 2cszA 76 -14.52 -5.17 7.67e+00 1lwdA 413 -12.80 -5.15 7.81e+00 1udh 244 -13.20 -5.01 9.09e+00 1k28D 391 -13.40 -4.96 9.58e+00 1yk3A 210 -12.31 -4.88 1.05e+01 1wf9A 107 -12.65 -4.86 1.08e+01 1g0hA 252 -13.74 -4.85 1.08e+01 1humA 69 -12.37 -4.82 1.12e+01 1b6rA 355 -12.64 -4.70 1.28e+01 1iznA 286 -13.20 -4.64 1.37e+01 1g8oA 310 -12.25 -4.63 1.39e+01 2bl5A 140 -11.89 -4.57 1.47e+01 1udg 244 -12.86 -4.57 1.47e+01 1zmbA 290 -14.71 -4.51 1.57e+01 1t71A 281 -12.53 -4.51 1.57e+01 1clc 639 -13.16 -4.51 1.58e+01 1lldA 319 -12.38 -4.41 1.76e+01 1ny6A 267 -12.42 -4.40 1.79e+01 1dl6A 58 -14.43 -4.39 1.80e+01 2bsdA 264 -12.99 -4.39 1.80e+01 1yc5A 246 -12.39 -4.37 1.84e+01 1rlyA 60 -14.63 -4.37 1.84e+01 1ui0A 205 -12.04 -4.36 1.87e+01 1y4lA 121 -13.20 -4.36 1.87e+01 1lzlA 323 -13.25 -4.33 1.93e+01 1twdA 256 -12.34 -4.32 1.96e+01 1meyC 87 -12.92 -4.32 1.96e+01 1k1gA 131 -13.50 -4.32 1.96e+01 2eveA 157 -12.30 -4.29 2.01e+01 1e1oA 504 -12.25 -4.26 2.10e+01 1dxrC 336 -12.41 -4.22 2.19e+01 1ois 223 -13.08 -4.19 2.26e+01 1ia9A 280 -12.61 -4.14 2.40e+01 1ff9A 450 -12.57 -4.13 2.43e+01 1oyc 400 -13.10 -4.10 2.50e+01 1oya 400 -13.10 -4.09 2.55e+01 1ppa 121 -13.74 -4.08 2.55e+01 1oyb 400 -13.10 -4.08 2.55e+01 1vqvA 306 -12.47 -4.08 2.56e+01 1pbyC 79 -12.16 -4.04 2.67e+01 1tfi 50 -11.96 -4.03 2.72e+01 1scs 237 -12.65 -4.02 2.73e+01 1nls 237 -12.65 -4.02 2.74e+01 6prcC 336 -12.19 -4.00 2.82e+01 1q41A 424 -12.14 -3.99 2.84e+01 1jjuC 79 -12.12 -3.96 2.95e+01 1j1bA 420 -12.05 -3.89 3.18e+01 1tzpA 255 -12.71 -3.83 3.41e+01 1mtnC 97 -11.38 -3.82 3.44e+01 2a4hA 126 -11.70 -3.82 3.44e+01 1jmxG 79 -11.72 -3.79 3.57e+01 1h70A 255 -12.09 -3.79 3.60e+01 1s8iA 121 -13.58 -3.78 3.60e+01 1u3wA 374 -12.27 -3.78 3.63e+01 1f75A 249 -11.48 -3.77 3.65e+01 1b6sA 355 -11.78 -3.77 3.65e+01 1i81A 83 -11.34 -3.76 3.71e+01 1qw2A 102 -10.86 -3.75 3.75e+01 1nbcA 155 -11.70 -3.73 3.83e+01 1jpdX 324 -11.30 -3.70 3.97e+01