% 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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR023W.t2k-100-40-40-str2+CB_burial_14_7 Host: farm16.cse.ucsc.edu Sun Mar 19 18:03:03 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR023W % --------------------------------------------------------------------- % 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 YGR023W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.400 File YGR023W.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YGR023W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 552 nodes, 982.04 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(=0.8986) * Reverse)^tau(=0.8349))) % 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 1yo8A 634 -66.41 -26.31 8.95e-03 1p30A 952 -57.96 -17.29 5.65e-01 1ehkB 168 -39.82 -17.03 6.38e-01 1dhx 967 -78.47 -15.73 1.19e+00 1ospO 257 -58.42 -13.69 3.25e+00 2aujD 309 -48.60 -13.55 3.48e+00 1p2zA 968 -53.01 -13.21 4.12e+00 1o6lA 337 -31.11 -13.00 4.57e+00 2fflA 756 -39.13 -12.98 4.63e+00 1gg6B 131 -50.47 -12.90 4.81e+00 1ruxA 951 -56.68 -12.83 4.99e+00 2cavA 445 -42.80 -12.63 5.50e+00 1ib8A 164 -38.55 -12.52 5.82e+00 1s4cA 155 -39.26 -12.43 6.10e+00 1dkgA 197 -29.16 -12.42 6.12e+00 2cas 548 -66.97 -12.14 7.04e+00 1w9zA 283 -33.24 -12.14 7.06e+00 1vgyA 393 -27.66 -12.11 7.17e+00 1yphC 131 -49.26 -12.09 7.24e+00 2bvcA 486 -34.56 -11.71 8.75e+00 1w99A 558 -37.02 -11.69 8.84e+00 4dpvZ 584 -63.86 -11.65 9.05e+00 1jopA 155 -37.72 -11.63 9.11e+00 1dmuA 299 -28.31 -11.59 9.31e+00 1ezvE 185 -37.68 -11.52 9.65e+00 1b9mA 265 -29.59 -11.45 1.00e+01 1div 149 -27.90 -11.44 1.00e+01 1lrzA 426 -25.93 -11.39 1.03e+01 2azeB 106 -34.82 -11.31 1.07e+01 1yarO 237 -26.84 -11.27 1.10e+01 1d8iA 311 -44.16 -11.26 1.10e+01 1l9mA 692 -35.24 -11.18 1.15e+01 1dih 273 -25.72 -11.16 1.16e+01 1t5eA 360 -35.56 -11.03 1.24e+01 1bsmA 201 -25.30 -11.01 1.25e+01 1bqhG 129 -47.26 -10.93 1.31e+01 1x82A 190 -31.21 -10.90 1.32e+01 2f86B 143 -31.28 -10.89 1.34e+01 1avmA 201 -25.24 -10.83 1.38e+01 1bccE 196 -40.70 -10.82 1.38e+01 1dkgB 197 -27.18 -10.79 1.40e+01 2bvyA 475 -30.41 -10.77 1.42e+01 1occG 84 -36.28 -10.64 1.51e+01 1jn5B 250 -30.91 -10.62 1.53e+01 1vjjA 692 -34.96 -10.61 1.54e+01 1p7gA 222 -25.74 -10.58 1.57e+01 1jk7A 323 -23.69 -10.43 1.69e+01 2f1fA 164 -28.05 -10.43 1.69e+01 1h4vB 421 -28.91 -10.30 1.81e+01 1nnvA 110 -32.88 -10.25 1.85e+01 1v25A 541 -28.25 -10.13 1.97e+01 1vqoB 338 -36.23 -10.09 2.02e+01 1s72B 338 -36.41 -10.02 2.10e+01 2eifA 136 -47.56 -9.99 2.13e+01 1fd9A 213 -33.38 -9.97 2.15e+01 1a6cA 513 -42.48 -9.95 2.16e+01 2ffuA 501 -32.31 -9.89 2.23e+01 1jj2B 337 -35.92 -9.84 2.30e+01 1jkgB 250 -30.40 -9.78 2.37e+01 2occG 84 -36.17 -9.76 2.39e+01 1azsA 220 -23.15 -9.75 2.41e+01 1v87A 114 -32.65 -9.69 2.49e+01 1drw 273 -24.07 -9.62 2.58e+01 1vqoX 92 -24.79 -9.60 2.60e+01 1kgyA 181 -43.84 -9.57 2.64e+01 1vf7A 369 -34.02 -9.57 2.64e+01 1culA 217 -22.88 -9.55 2.67e+01 1k28A 584 -89.60 -9.51 2.73e+01 1iuhA 198 -32.22 -9.48 2.78e+01 1cgo 127 -21.88 -9.40 2.89e+01 1qvcA 145 -52.83 -9.40 2.90e+01 1o4yA 288 -27.65 -9.38 2.92e+01 1jj2L 194 -37.71 -9.37 2.94e+01 1u32A 293 -22.02 -9.35 2.96e+01 1p4cA 380 -25.71 -9.35 2.97e+01 1k24A 253 -30.83 -9.34 2.98e+01 1o7nB 194 -34.63 -9.31 3.04e+01 1fzdA 201 -23.13 -9.26 3.11e+01 1sva1 361 -70.94 -9.23 3.16e+01 1l6rA 227 -22.37 -9.21 3.20e+01 1hkxA 147 -33.56 -9.20 3.22e+01 1q40B 219 -37.56 -9.18 3.26e+01 1q42A 201 -35.00 -9.16 3.29e+01 1pf4A 582 -41.49 -9.16 3.29e+01 1gm5A 780 -35.38 -9.14 3.32e+01 1v54G 85 -35.76 -9.13 3.33e+01 1odeA 122 -24.64 -9.12 3.35e+01 2bydA 323 -28.37 -9.03 3.52e+01 2atfA 200 -31.07 -9.01 3.56e+01 2occB 227 -37.50 -9.00 3.56e+01 1fouA 309 -35.06 -9.00 3.57e+01 1yx1A 264 -20.65 -9.00 3.57e+01 2cvhA 220 -23.73 -8.99 3.58e+01 1smvA 260 -30.11 -8.96 3.64e+01 1g3gA 164 -40.19 -8.96 3.64e+01 1uldA 150 -36.08 -8.96 3.65e+01 2fmlA 273 -27.92 -8.94 3.68e+01 1g87A 614 -24.58 -8.93 3.70e+01 1ndoB 194 -34.59 -8.90 3.76e+01 2a6hE 99 -28.10 -8.85 3.87e+01 1psuA 140 -23.55 -8.85 3.88e+01 1gbg 214 -27.89 -8.84 3.90e+01 1v54B 227 -36.75 -8.79 3.99e+01 2cr5A 109 -43.90 -8.79 3.99e+01