% 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.YEL012W.t2k-100-30-stride-ebghtl Host: farm09 Fri Nov 18 19:16:50 2005 % karplus Dir: /projects/compbiousr/compbio0404/experiments/protein-predict/yeast/YEL0/YEL012W % --------------------------------------------------------------------- % 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 YEL012W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL012W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13048 sequences, 3092733 residues, 219 nodes, 341.10 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(=1.0852) * Reverse)^tau(=0.8723))) % 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 1x23A 155 -212.11 -192.22 1.67e-42 1z2uA 150 -214.20 -189.64 5.76e-42 2ayvA 166 -208.15 -187.90 1.33e-41 1y6lA 149 -200.44 -182.64 1.67e-40 2bepA 159 -185.54 -169.44 9.98e-38 1jatA 155 -189.15 -168.21 1.82e-37 1jbbA 153 -189.88 -168.17 1.85e-37 1yh2A 175 -182.60 -166.03 5.25e-37 1u9aA 160 -182.73 -164.85 9.34e-37 2e2c 156 -181.48 -164.54 1.09e-36 1fzyA 149 -182.24 -164.12 1.33e-36 2ucz 165 -185.42 -159.56 1.24e-35 1i7kA 179 -172.29 -156.65 5.19e-35 1fxtA 149 -173.14 -156.11 6.77e-35 1zdnA 158 -168.29 -149.47 1.79e-33 1yh6A 179 -161.49 -146.20 9.00e-33 1yrvA 169 -155.03 -142.22 6.50e-32 1wzvA 155 -158.58 -140.39 1.62e-31 1yf9A 171 -153.09 -138.43 4.31e-31 2awfA 172 -153.17 -132.97 6.62e-30 2a4dA 160 -132.63 -112.70 1.92e-25 1j7dA 145 -130.24 -108.82 1.41e-24 1jatB 138 -120.09 -105.03 9.96e-24 1zuoA 186 -92.66 -77.38 2.11e-17 1uzxA 169 -42.56 -27.59 4.13e-05 1s1qA 145 -42.78 -27.27 5.02e-05 1kppA 145 -39.98 -25.16 1.85e-04 2ac3A 316 -29.85 -16.92 3.49e-02 1ukxA 137 -24.88 -13.87 2.61e-01 2ac5A 316 -25.01 -13.67 2.99e-01 1ywzA 175 -26.29 -13.08 4.44e-01 2bi7A 384 -23.55 -11.63 1.19e+00 1t5eA 360 -24.58 -11.54 1.27e+00 1i8kB 124 -20.13 -11.39 1.41e+00 1w9hA 427 -24.06 -11.36 1.43e+00 1srqA 341 -22.58 -11.06 1.76e+00 1ny9A 143 -22.77 -10.55 2.51e+00 1h3fA 432 -23.51 -10.34 2.89e+00 1vf7A 369 -23.41 -10.31 2.97e+00 2es9A 115 -25.38 -10.26 3.07e+00 1usuA 260 -24.00 -10.15 3.31e+00 1a2yB 116 -19.23 -10.05 3.56e+00 1kbhB 59 -20.43 -10.00 3.68e+00 1h3oB 76 -22.22 -9.58 4.94e+00 1mkeA 152 -19.28 -9.37 5.72e+00 1ezvH 74 -22.46 -9.37 5.73e+00 2biiA 424 -18.73 -9.28 6.10e+00 1eqfA 280 -24.25 -9.21 6.38e+00 1l0qA 391 -19.51 -9.14 6.70e+00 1chrA 370 -21.15 -9.09 6.94e+00 1v0jA 399 -22.05 -9.09 6.96e+00 1bp3B 211 -19.14 -9.09 6.97e+00 1qhtA 775 -24.16 -9.09 6.98e+00 2auaA 224 -20.20 -9.04 7.22e+00 1vfaB 116 -18.21 -9.01 7.35e+00 1g7jB 116 -18.21 -9.01 7.35e+00 1xaoA 121 -20.78 -8.94 7.76e+00 6gsvA 217 -21.55 -8.93 7.81e+00 1i5nA 146 -22.31 -8.78 8.64e+00 1winA 143 -21.13 -8.76 8.81e+00 1yqcA 170 -18.21 -8.66 9.41e+00 1jpzA 473 -23.51 -8.61 9.77e+00 2bmhA 455 -24.13 -8.59 9.88e+00 1eyvA 156 -21.32 -8.50 1.06e+01 1y7rA 133 -18.56 -8.49 1.07e+01 2bnxA 386 -22.44 -8.40 1.13e+01 1cdi 179 -19.47 -8.23 1.28e+01 1aa0 113 -18.81 -8.18 1.32e+01 1c1kA 217 -24.40 -8.18 1.33e+01 1cd9C 175 -22.64 -8.02 1.49e+01 1tgoA 773 -22.87 -8.00 1.51e+01 1qnoA 344 -20.51 -7.97 1.54e+01 1fohA 664 -20.25 -7.93 1.59e+01 1xkrA 206 -18.64 -7.86 1.68e+01 1jj2L 194 -19.09 -7.80 1.75e+01 1fcdC 174 -22.78 -7.77 1.79e+01 1ugjA 141 -17.55 -7.77 1.79e+01 2ae6A 166 -18.19 -7.74 1.82e+01 1kb9F 74 -21.18 -7.72 1.85e+01 1jj2M 186 -19.38 -7.70 1.87e+01 1rcd 173 -24.30 -7.58 2.05e+01 1s72N 187 -19.22 -7.56 2.08e+01 1pnsB 234 -21.40 -7.56 2.08e+01 1mqkH 127 -16.20 -7.54 2.10e+01 1j5eB 256 -21.31 -7.53 2.13e+01 1i8tA 367 -20.76 -7.50 2.17e+01 1gtkA 313 -17.69 -7.46 2.23e+01 1who 96 -18.41 -7.40 2.33e+01 1wteA 272 -19.79 -7.38 2.36e+01 1ysc 421 -20.11 -7.36 2.39e+01 1oaqH 121 -16.08 -7.32 2.47e+01 1qqcA 773 -22.04 -7.28 2.53e+01 1qnrA 344 -19.85 -7.28 2.54e+01 1pda 315 -17.25 -7.24 2.62e+01 1ug8A 87 -17.59 -7.22 2.66e+01 1c4kA 730 -19.61 -7.21 2.68e+01 1ezfA 340 -20.46 -7.15 2.80e+01 1bfa 134 -18.80 -7.12 2.86e+01 1tafA 68 -17.94 -7.11 2.88e+01 1j05B 121 -16.05 -7.08 2.95e+01 1pn0A 665 -19.89 -7.07 2.95e+01 1bea 127 -18.70 -7.03 3.05e+01 1u0fA 564 -19.07 -7.01 3.10e+01 1llnA 262 -20.52 -6.96 3.21e+01 1hilB 220 -15.98 -6.86 3.44e+01 1qrdA 273 -18.48 -6.85 3.46e+01 1ks8A 433 -23.39 -6.85 3.47e+01 1t2jA 116 -15.51 -6.84 3.50e+01 1qgiA 259 -18.76 -6.83 3.53e+01 1sedA 117 -20.07 -6.74 3.76e+01 1wloA 136 -19.84 -6.73 3.78e+01 1rt8A 513 -21.59 -6.70 3.87e+01 1nekC 129 -18.98 -6.69 3.91e+01 1w4xA 542 -20.15 -6.69 3.92e+01