% 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. % --------------------------------------------------------------------- % str2foo.1.YGR035W-A.t2k-100-30-str2 Host: farm09.cse.ucsc.edu Sun Feb 12 21:51:30 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.str2s % % 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.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13614 sequences, 3208521 residues, 74 nodes, 118.15 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(=2.3844) * Reverse)^tau(=0.7785))) % 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 -17.06 -9.34 1.50e-01 1aayA 90 -17.04 -9.33 1.51e-01 1udh 244 -17.88 -8.94 2.18e-01 1tc5A 194 -17.04 -8.94 2.20e-01 1a1iA 90 -16.39 -8.67 2.84e-01 1g2fC 90 -15.74 -8.28 4.11e-01 1lldA 319 -15.63 -7.52 8.57e-01 4rxn 54 -17.50 -7.28 1.09e+00 2cszA 76 -16.25 -6.98 1.46e+00 1jnrB 150 -15.77 -6.74 1.85e+00 1udg 244 -15.10 -6.58 2.18e+00 1xaoA 121 -13.96 -6.46 2.47e+00 2ashA 381 -14.62 -6.41 2.60e+00 1llmC 88 -13.40 -6.34 2.79e+00 1uyjA 296 -14.97 -6.33 2.82e+00 1yc61 154 -14.14 -6.16 3.33e+00 1plfA 72 -13.85 -6.12 3.47e+00 1f75A 249 -13.71 -6.00 3.96e+00 1wf9A 107 -13.87 -5.93 4.23e+00 1m3sA 186 -13.61 -5.89 4.43e+00 1iro 54 -16.19 -5.81 4.80e+00 1tqnA 486 -14.54 -5.76 5.03e+00 2bsdA 264 -14.11 -5.74 5.16e+00 1hn6A 110 -14.80 -5.73 5.22e+00 1xxsA 122 -14.30 -5.72 5.28e+00 1ui0A 205 -13.43 -5.65 5.65e+00 1vajA 214 -14.02 -5.60 5.94e+00 1wthD 391 -13.93 -5.49 6.70e+00 1dl6A 58 -14.37 -5.44 7.03e+00 1clc 639 -13.99 -5.41 7.25e+00 1humA 69 -12.89 -5.33 7.95e+00 1qlaB 239 -14.34 -5.32 7.98e+00 1rlyA 60 -14.65 -5.24 8.73e+00 1f7tA 122 -12.66 -5.23 8.78e+00 1zmbA 290 -15.36 -5.21 9.01e+00 1lzlA 323 -14.19 -5.20 9.08e+00 1ddgA 374 -13.24 -5.18 9.30e+00 2aw4Z 70 -13.58 -5.17 9.38e+00 1s48A 609 -13.10 -5.03 1.08e+01 1frrA 95 -12.48 -4.99 1.13e+01 1oya 400 -13.71 -4.98 1.14e+01 1oyb 400 -13.71 -4.98 1.15e+01 1y4lA 121 -13.42 -4.89 1.27e+01 1oyc 400 -13.72 -4.88 1.28e+01 1h70A 255 -14.27 -4.85 1.32e+01 1q41A 424 -13.06 -4.84 1.33e+01 1j1bA 420 -13.02 -4.84 1.33e+01 2b25A 336 -12.82 -4.80 1.40e+01 1k92A 455 -12.26 -4.77 1.44e+01 1jp3A 253 -12.41 -4.72 1.52e+01 1uehA 253 -12.41 -4.71 1.53e+01 1zcjA 463 -13.39 -4.68 1.59e+01 2anwA 241 -13.06 -4.67 1.60e+01 1qwtA 255 -13.17 -4.65 1.64e+01 1g8oA 310 -13.61 -4.63 1.67e+01 1lylA 504 -12.80 -4.62 1.70e+01 1bllE 488 -12.19 -4.57 1.78e+01 1a7tA 232 -12.64 -4.50 1.94e+01 1elt 236 -13.20 -4.50 1.94e+01 1lam 484 -12.11 -4.49 1.95e+01 1iznA 286 -12.92 -4.47 1.99e+01 1e1oA 504 -12.72 -4.47 1.99e+01 1e0cA 271 -12.08 -4.47 1.99e+01 1i7nA 309 -12.35 -4.47 1.99e+01 2a3nA 355 -12.33 -4.43 2.08e+01 1prcC 336 -12.64 -4.42 2.10e+01 1lap 488 -12.05 -4.42 2.11e+01 1mtnC 97 -12.10 -4.42 2.11e+01 1lwdA 413 -11.79 -4.41 2.14e+01 1yc5A 246 -12.56 -4.38 2.21e+01 1ff9A 450 -12.36 -4.37 2.23e+01 1t3nA 388 -12.25 -4.33 2.34e+01 2f4lA 297 -13.49 -4.32 2.36e+01 1i81A 83 -11.66 -4.30 2.42e+01 1nepA 130 -13.65 -4.25 2.55e+01 1ox0A 430 -12.07 -4.25 2.55e+01 1fonA 240 -13.53 -4.25 2.55e+01 1ff4A 65 -11.66 -4.25 2.56e+01 1agy 200 -12.40 -4.23 2.60e+01 1gg6C 97 -11.94 -4.22 2.63e+01 1uxtA 501 -12.51 -4.21 2.66e+01 1ab9C 97 -11.87 -4.19 2.71e+01 1vqvA 306 -11.92 -4.19 2.73e+01 1cex 214 -12.33 -4.19 2.73e+01 1niyA 36 -11.86 -4.18 2.75e+01 1g0hA 252 -12.53 -4.17 2.78e+01 1taq 832 -13.30 -4.15 2.84e+01 2ah5A 210 -11.71 -4.14 2.89e+01 1jh3A 107 -11.62 -4.13 2.92e+01 1jpdX 324 -12.45 -4.11 2.99e+01 1tzpA 255 -12.62 -4.10 3.02e+01 1f7lA 121 -11.36 -4.10 3.02e+01 2anyA 241 -12.27 -4.09 3.03e+01 1ia9A 280 -12.44 -4.07 3.10e+01 1ffa 214 -12.25 -4.06 3.15e+01 1gtdA 85 -10.81 -4.06 3.15e+01 1mnnA 340 -12.18 -4.05 3.19e+01 1ni4A 365 -13.39 -4.03 3.25e+01 1k4tA 592 -12.12 -4.02 3.28e+01 1cus 200 -12.15 -4.02 3.29e+01 1ile 821 -12.67 -4.01 3.32e+01 1ppa 121 -13.16 -3.99 3.42e+01 1mgqA 83 -11.34 -3.98 3.43e+01 1ny6A 267 -11.78 -3.98 3.44e+01 1wjgA 137 -12.59 -3.98 3.45e+01 1npyA 271 -11.60 -3.96 3.51e+01 2bfwA 200 -11.40 -3.94 3.59e+01 1f20A 435 -12.05 -3.90 3.76e+01 1pxvA 183 -12.48 -3.85 3.97e+01