% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YCR102W-A.t2k-100-40-40-str2+CB_burial_14_7 Host: farm18 Mon Nov 29 12:19:46 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YCR1/YCR102W-A % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % 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 YCR102W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.400 File YCR102W-A.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YCR102W-A.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 66 nodes, 81.17 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 (0.00) % E-value on N (=10700) sequences: % N / (1 + exp(-(lambda(=1.1909) * Reverse)^tau(=0.8518))) % Calculated when Simple < simple_threshold (0.00) % 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 1q9jA 422 -20.98 -11.32 1.12e+00 1mc2A 122 -19.86 -10.57 1.88e+00 1ualA 274 -23.92 -10.52 1.94e+00 1ezvF 125 -21.10 -9.50 3.98e+00 1kb9G 125 -21.10 -9.49 4.00e+00 1rxr 83 -19.23 -9.48 4.03e+00 1kyoG 126 -20.78 -9.25 4.75e+00 1irl 133 -22.53 -9.11 5.25e+00 1ffkU 91 -21.47 -9.09 5.31e+00 1pszA 303 -19.06 -9.06 5.44e+00 1jj2W 91 -22.66 -9.05 5.47e+00 1s72X 92 -22.65 -9.04 5.50e+00 1jbwA 428 -19.03 -9.00 5.68e+00 1ofhA 310 -21.42 -8.99 5.72e+00 1dszB 85 -18.44 -8.98 5.76e+00 1hra 81 -18.75 -8.93 5.99e+00 2nllB 103 -19.17 -8.82 6.46e+00 1ewqA 765 -18.81 -8.68 7.15e+00 1kijA 390 -18.16 -8.62 7.45e+00 1mp1A 111 -21.48 -8.60 7.53e+00 1tk1A 260 -19.70 -8.51 8.06e+00 1fgs 428 -18.80 -8.44 8.47e+00 1g3kA 174 -18.37 -8.39 8.79e+00 2btfA 375 -17.90 -8.30 9.41e+00 1pyaB 228 -17.93 -8.19 1.02e+01 1lqtA 456 -17.73 -8.18 1.03e+01 1dkgD 383 -18.84 -8.16 1.04e+01 1h3oA 75 -16.97 -8.14 1.06e+01 1v2yA 105 -16.34 -8.12 1.07e+01 1dszA 86 -18.31 -8.09 1.09e+01 1k94A 165 -18.54 -8.02 1.15e+01 1k8kB 394 -18.24 -7.93 1.23e+01 1mn8A 100 -20.15 -7.92 1.24e+01 1fiqC 763 -16.46 -7.83 1.32e+01 1s8iA 121 -16.94 -7.72 1.43e+01 1ngkA 128 -21.70 -7.69 1.46e+01 1j0aA 325 -16.40 -7.62 1.54e+01 1ibvB 229 -17.28 -7.56 1.61e+01 1h4lD 147 -18.62 -7.55 1.62e+01 2nllA 66 -17.02 -7.51 1.67e+01 1h1lA 481 -16.76 -7.49 1.70e+01 1tk4A 121 -16.94 -7.46 1.72e+01 1g10A 102 -15.52 -7.38 1.83e+01 1aye 401 -15.65 -7.37 1.84e+01 1l5aA 436 -18.11 -7.37 1.85e+01 1amz 435 -17.43 -7.31 1.93e+01 1gntA 553 -17.03 -7.30 1.94e+01 1jroB 777 -15.55 -7.28 1.97e+01 1mkzA 172 -16.48 -7.27 1.99e+01 1n16A 381 -16.84 -7.22 2.07e+01 1ryaA 160 -15.34 -7.15 2.17e+01 4gr1 478 -16.86 -7.12 2.22e+01 3minC 491 -17.17 -7.10 2.25e+01 3grs 478 -16.90 -7.06 2.32e+01 1a6s 87 -16.65 -7.06 2.32e+01 1tj9A 121 -16.40 -7.00 2.43e+01 1gtxA 472 -16.92 -6.97 2.48e+01 1fv0A 121 -16.40 -6.96 2.49e+01 1e2uA 553 -16.82 -6.93 2.55e+01 1m5dA 263 -16.34 -6.92 2.57e+01 1te5A 257 -17.10 -6.91 2.60e+01 1csh 435 -17.00 -6.90 2.62e+01 1g41A 444 -19.69 -6.89 2.63e+01 1gr2A 279 -16.59 -6.87 2.66e+01 1e1dA 553 -17.05 -6.87 2.66e+01 1ppa 121 -15.84 -6.87 2.67e+01 2end 138 -18.63 -6.85 2.72e+01 1ulyA 192 -19.75 -6.84 2.72e+01 1rypL 212 -17.48 -6.83 2.74e+01 1fjgB 256 -17.01 -6.81 2.79e+01 1qh8A 478 -15.97 -6.80 2.80e+01 1ftkA 279 -16.10 -6.78 2.85e+01 1kpmA 121 -16.30 -6.76 2.89e+01 1qk4A 233 -15.97 -6.74 2.93e+01 1s8nA 205 -17.80 -6.73 2.96e+01 1l7dA 384 -15.49 -6.73 2.96e+01 1f4qA 165 -17.57 -6.73 2.97e+01 1g65K 211 -17.29 -6.70 3.02e+01 2minA 491 -16.38 -6.68 3.06e+01 1sqzA 121 -16.22 -6.68 3.08e+01 1cjbA 231 -16.71 -6.67 3.09e+01 1mqdA 261 -16.11 -6.66 3.13e+01 1h75A 81 -15.68 -6.63 3.19e+01 1vg8A 207 -16.37 -6.62 3.20e+01 1fsgA 233 -15.90 -6.62 3.21e+01 1hywA 68 -15.93 -6.57 3.32e+01 1pdo 135 -16.26 -6.57 3.32e+01 1im2A 444 -20.07 -6.56 3.37e+01 1tqjA 230 -15.84 -6.55 3.39e+01 1m1nA 491 -16.19 -6.55 3.40e+01 1mqiA 263 -16.01 -6.54 3.40e+01 1qguA 478 -15.73 -6.53 3.43e+01 1mo9A 523 -17.98 -6.41 3.76e+01 1jihA 531 -19.29 -6.40 3.78e+01 1jw3A 140 -16.43 -6.37 3.86e+01 1anv 356 -16.63 -6.34 3.95e+01 1rvgA 305 -17.44 -6.33 3.98e+01