% 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. % --------------------------------------------------------------------- % dsspfoo.1.YGR035W-A.t2k-100-30-dssp-ebghstl Host: farm09.cse.ucsc.edu Sun Feb 12 21:55:54 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-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13614 sequences, 3208521 residues, 74 nodes, 118.41 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(=2.4232) * Reverse)^tau(=0.7734))) % 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 -16.32 -8.59 3.16e-01 1aayA 90 -16.29 -8.57 3.20e-01 1tc5A 194 -16.68 -8.52 3.36e-01 1a1iA 90 -15.79 -8.01 5.46e-01 1g2fC 90 -15.25 -7.73 7.14e-01 1jnrB 150 -16.50 -7.68 7.49e-01 1wthD 391 -15.66 -7.53 8.65e-01 1lldA 319 -15.52 -7.50 8.96e-01 1udh 244 -16.06 -7.31 1.08e+00 2ashA 381 -15.31 -7.16 1.24e+00 2cszA 76 -15.98 -6.86 1.67e+00 1uyjA 296 -14.96 -6.71 1.93e+00 1xaoA 121 -14.26 -6.63 2.10e+00 1plfA 72 -14.53 -6.59 2.20e+00 1tqnA 486 -14.97 -6.48 2.45e+00 4rxn 54 -16.47 -6.43 2.56e+00 1yc61 154 -14.19 -6.27 3.03e+00 1llmC 88 -13.15 -6.14 3.43e+00 1hn6A 110 -15.14 -6.07 3.70e+00 1m3sA 186 -13.45 -5.87 4.53e+00 1dl6A 58 -15.15 -5.85 4.62e+00 1humA 69 -13.42 -5.82 4.77e+00 1oyb 400 -14.85 -5.78 4.98e+00 1oya 400 -14.85 -5.78 4.99e+00 1oyc 400 -14.85 -5.71 5.34e+00 1f75A 249 -13.21 -5.58 6.09e+00 1clc 639 -13.97 -5.55 6.31e+00 1ui0A 205 -13.04 -5.51 6.56e+00 1s48A 609 -13.30 -5.50 6.67e+00 1qlaB 239 -13.97 -5.46 6.92e+00 1elt 236 -13.83 -5.41 7.30e+00 1udg 244 -13.50 -5.41 7.30e+00 2aw4Z 70 -13.83 -5.40 7.41e+00 1wf9A 107 -13.20 -5.17 9.43e+00 2bsdA 264 -13.59 -5.15 9.61e+00 1rlyA 60 -14.98 -5.02 1.10e+01 1iro 54 -15.17 -4.99 1.14e+01 1ff9A 450 -12.93 -4.94 1.20e+01 1zcjA 463 -13.26 -4.93 1.21e+01 1t3nA 388 -12.58 -4.92 1.22e+01 1g8oA 310 -13.31 -4.92 1.23e+01 1xxsA 122 -13.42 -4.87 1.29e+01 1taq 832 -13.80 -4.85 1.32e+01 1vajA 214 -12.95 -4.79 1.40e+01 1iznA 286 -13.21 -4.79 1.41e+01 1prcC 336 -12.89 -4.76 1.45e+01 1twdA 256 -12.88 -4.76 1.46e+01 1fonA 240 -13.83 -4.73 1.50e+01 1k92A 455 -12.05 -4.69 1.57e+01 1e0cA 271 -12.27 -4.63 1.68e+01 1f7tA 122 -12.04 -4.61 1.71e+01 1q41A 424 -12.64 -4.60 1.73e+01 1zmbA 290 -15.05 -4.57 1.78e+01 1qwtA 255 -13.09 -4.57 1.79e+01 1cus 200 -12.75 -4.56 1.80e+01 2a9mL 110 -11.86 -4.55 1.82e+01 2b25A 336 -12.65 -4.55 1.82e+01 1agy 200 -12.75 -4.54 1.85e+01 1ile 821 -13.00 -4.52 1.88e+01 1mtnC 97 -12.00 -4.50 1.92e+01 1ffa 214 -12.86 -4.46 2.01e+01 1i7nA 309 -12.27 -4.45 2.03e+01 1lwdA 413 -11.84 -4.45 2.03e+01 1k4gA 386 -13.22 -4.41 2.13e+01 1de6A 426 -13.32 -4.41 2.13e+01 1j93A 353 -13.71 -4.41 2.14e+01 1k1gA 131 -13.44 -4.39 2.18e+01 1g0hA 252 -12.95 -4.39 2.18e+01 1cqxA 403 -12.07 -4.38 2.21e+01 1de5A 426 -13.42 -4.37 2.22e+01 1r5yA 386 -13.31 -4.37 2.23e+01 2f4lA 297 -12.99 -4.35 2.27e+01 1y4lA 121 -12.77 -4.35 2.27e+01 1qw2A 102 -11.29 -4.34 2.29e+01 1a0hA 159 -13.04 -4.33 2.32e+01 1nbcA 155 -12.15 -4.31 2.36e+01 1cex 214 -12.69 -4.29 2.41e+01 1i81A 83 -11.54 -4.28 2.46e+01 1b8sA 504 -12.37 -4.27 2.49e+01 1j1bA 420 -12.25 -4.27 2.49e+01 1ny6A 267 -12.01 -4.24 2.55e+01 1niyA 36 -11.88 -4.23 2.59e+01 1k28D 391 -12.58 -4.22 2.61e+01 1ddgA 374 -12.46 -4.21 2.66e+01 1ab9C 97 -11.65 -4.19 2.72e+01 2eveA 157 -12.31 -4.18 2.75e+01 1ijhA 504 -12.23 -4.17 2.78e+01 1k4tA 592 -11.97 -4.16 2.79e+01 1lylA 504 -12.04 -4.16 2.80e+01 1gg6C 97 -11.72 -4.16 2.80e+01 1eq9A 222 -12.72 -4.16 2.80e+01 1a7tA 232 -12.44 -4.16 2.81e+01 1cot 129 -12.09 -4.15 2.83e+01 1mgqA 83 -11.38 -4.15 2.84e+01 1mxtA 504 -12.22 -4.15 2.84e+01 1uehA 253 -11.94 -4.13 2.88e+01 1b4vA 504 -12.22 -4.12 2.91e+01 1c2rA 116 -11.89 -4.12 2.93e+01 1zroA 602 -11.89 -4.12 2.94e+01 2anwA 241 -12.51 -4.11 2.97e+01 1jp3A 253 -11.93 -4.11 2.98e+01 1pud 386 -12.88 -4.10 2.98e+01 1cm9A 74 -12.36 -4.10 2.99e+01 1n1pA 504 -12.17 -4.10 3.00e+01 1n4wA 504 -12.17 -4.10 3.00e+01 1cuj 214 -12.39 -4.10 3.00e+01 1vydA 116 -11.91 -4.08 3.05e+01 1ujnA 348 -12.64 -4.08 3.08e+01 1uxtA 501 -12.27 -4.07 3.09e+01 1co4A 42 -11.89 -4.06 3.13e+01 1tx4B 178 -12.48 -4.06 3.13e+01 2a3nA 355 -11.75 -4.05 3.16e+01 1mnnA 340 -12.09 -4.05 3.16e+01 1kmqA 184 -12.56 -4.05 3.17e+01 1ox0A 430 -12.03 -4.04 3.20e+01 1kewA 361 -11.72 -4.02 3.27e+01 1ko3A 230 -13.46 -4.01 3.30e+01 1jndA 420 -12.06 -3.98 3.40e+01 2bl5A 140 -11.42 -3.97 3.45e+01 2eiaB 206 -11.00 -3.95 3.53e+01 1pxgA 382 -13.30 -3.95 3.54e+01 1eia 207 -10.97 -3.94 3.58e+01 1e1oA 504 -11.88 -3.93 3.63e+01 2a8nA 144 -11.94 -3.92 3.65e+01 1jh3A 107 -11.45 -3.91 3.70e+01 1jpdX 324 -12.13 -3.91 3.70e+01 1smrA 335 -12.77 -3.90 3.73e+01 1jlyA 304 -11.84 -3.89 3.77e+01 1a36A 592 -11.67 -3.89 3.79e+01 2a4hA 126 -11.66 -3.89 3.80e+01 1lam 484 -11.57 -3.89 3.80e+01 1jlxA 304 -11.85 -3.88 3.82e+01 1wjgA 137 -12.46 -3.87 3.85e+01 1dxrC 336 -12.27 -3.87 3.86e+01 1kyhA 276 -13.08 -3.86 3.91e+01 1pmnA 364 -11.55 -3.86 3.92e+01 1lap 488 -11.55 -3.85 3.95e+01 1bllE 488 -11.55 -3.84 3.99e+01