% 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. % --------------------------------------------------------------------- % stridefoo.1.YGR035W-A.t2k-100-30-stride-ebghtl Host: farm09.cse.ucsc.edu Sun Feb 12 22:00:18 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.2ds % % 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.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13614 sequences, 3208521 residues, 74 nodes, 117.71 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(=2.4070) * Reverse)^tau(=0.7743))) % 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 -18.10 -10.30 6.66e-02 1aayA 90 -18.07 -10.29 6.73e-02 1a1iA 90 -18.00 -10.21 7.25e-02 1g2fC 90 -16.80 -8.96 2.28e-01 1wthD 391 -16.02 -7.83 6.65e-01 1llmC 88 -14.61 -7.21 1.21e+00 1jnrB 150 -15.62 -6.80 1.81e+00 2cszA 76 -16.37 -6.47 2.51e+00 1tqnA 486 -14.88 -6.44 2.61e+00 1k28D 391 -14.56 -6.32 2.92e+00 2ashA 381 -14.64 -6.24 3.18e+00 1tc5A 194 -14.30 -6.10 3.65e+00 1udh 244 -14.57 -6.00 4.03e+00 1udg 244 -14.57 -6.00 4.03e+00 1vkbA 161 -14.66 -5.99 4.09e+00 1jilA 420 -13.99 -5.94 4.31e+00 1e1oA 504 -13.43 -5.63 5.90e+00 1wf9A 107 -13.41 -5.58 6.24e+00 1lldA 319 -13.60 -5.44 7.23e+00 4rxn 54 -16.10 -5.42 7.39e+00 1plfA 72 -13.38 -5.41 7.48e+00 1xaoA 121 -13.25 -5.34 8.00e+00 1lylA 504 -13.07 -5.31 8.28e+00 1humA 69 -13.07 -5.26 8.68e+00 1taq 832 -13.63 -5.26 8.72e+00 1yc61 154 -12.96 -5.18 9.49e+00 1g8oA 310 -13.41 -5.14 9.91e+00 1uyjA 296 -13.38 -5.13 9.96e+00 1g0hA 252 -14.08 -5.13 1.00e+01 1yc5A 246 -13.32 -5.12 1.01e+01 1vajA 214 -13.26 -5.12 1.01e+01 1qlaB 239 -14.14 -5.03 1.11e+01 1tvdA 116 -13.14 -5.01 1.13e+01 1t71A 281 -12.96 -4.96 1.20e+01 1lwdA 413 -12.32 -4.92 1.25e+01 1zcjA 463 -13.29 -4.86 1.33e+01 1dl6A 58 -14.93 -4.78 1.45e+01 1scs 237 -12.90 -4.72 1.56e+01 1rlyA 60 -15.13 -4.68 1.61e+01 1hn6A 110 -14.12 -4.65 1.68e+01 1bu8A 452 -15.87 -4.61 1.74e+01 1clc 639 -13.03 -4.61 1.74e+01 1m3sA 186 -12.27 -4.60 1.75e+01 1k92A 455 -12.01 -4.60 1.76e+01 1ui0A 205 -12.15 -4.56 1.84e+01 2b25A 336 -12.93 -4.56 1.84e+01 1f75A 249 -12.30 -4.56 1.84e+01 1xxsA 122 -13.00 -4.54 1.88e+01 1vqvA 306 -12.45 -4.50 1.95e+01 1nls 237 -12.77 -4.50 1.96e+01 1tzpA 255 -12.93 -4.49 1.99e+01 1wgeA 83 -13.95 -4.42 2.14e+01 1zmbA 290 -14.49 -4.38 2.24e+01 1meyC 87 -13.02 -4.38 2.25e+01 1oya 400 -12.92 -4.37 2.25e+01 1de6A 426 -13.22 -4.35 2.31e+01 1mroB 442 -12.59 -4.32 2.38e+01 1ois 223 -14.06 -4.32 2.39e+01 1de5A 426 -13.22 -4.26 2.54e+01 1mxtA 504 -12.25 -4.24 2.60e+01 1n1pA 504 -12.25 -4.24 2.60e+01 1n4wA 504 -12.25 -4.24 2.60e+01 1loi 26 -11.56 -4.23 2.63e+01 1y4lA 121 -12.33 -4.23 2.65e+01 1jjuC 79 -12.22 -4.22 2.68e+01 1b8sA 504 -12.19 -4.21 2.69e+01 1pbyC 79 -12.23 -4.20 2.72e+01 1a0hA 159 -13.75 -4.19 2.74e+01 1b4vA 504 -12.16 -4.18 2.77e+01 1ijhA 504 -12.16 -4.18 2.78e+01 1twdA 256 -12.11 -4.17 2.83e+01 1iro 54 -14.82 -4.14 2.90e+01 1s48A 609 -12.60 -4.14 2.91e+01 1ny6A 267 -11.91 -4.14 2.92e+01 1jmxG 79 -12.10 -4.14 2.93e+01 1oyc 400 -12.71 -4.12 2.98e+01 1vizA 240 -12.03 -4.12 2.99e+01 1w36C 1122 -12.70 -4.11 3.00e+01 1oyb 400 -12.70 -4.11 3.01e+01 1q41A 424 -13.25 -4.09 3.07e+01 1pmnA 364 -11.74 -4.08 3.11e+01 1hbnB 442 -12.27 -4.03 3.30e+01 1j1bA 420 -13.26 -4.02 3.33e+01 2bsdA 264 -12.69 -4.01 3.38e+01 2aw4Z 70 -14.27 -3.99 3.45e+01 2b9hA 353 -11.90 -3.95 3.59e+01 1u0mA 382 -12.04 -3.90 3.79e+01 1lzlA 323 -13.02 -3.90 3.81e+01 2eveA 157 -11.88 -3.88 3.88e+01 1mnnA 340 -12.01 -3.87 3.92e+01 1ff9A 450 -11.45 -3.87 3.93e+01 1rc9A 221 -12.28 -3.87 3.94e+01 1n45A 233 -11.72 -3.86 3.96e+01