% 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.YGR236C.t2k-100-30-dssp-ebghstl Host: farm16.cse.ucsc.edu Fri Mar 3 08:44:09 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR236C % --------------------------------------------------------------------- % 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 YGR236C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR236C.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14381 sequences, 3373755 residues, 96 nodes, 159.76 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(=2.7508) * Reverse)^tau(=0.7191))) % 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 1nt4A 391 -17.21 -8.07 1.02e+00 1m6dA 214 -16.00 -7.93 1.13e+00 1eni 138 -16.55 -7.72 1.36e+00 1exbA 332 -16.36 -7.65 1.44e+00 1enk 138 -16.45 -7.60 1.51e+00 1r5zA 323 -16.89 -7.55 1.57e+00 2end 138 -16.41 -7.54 1.58e+00 1vasA 137 -16.43 -7.48 1.66e+00 1zsxA 347 -16.24 -7.47 1.67e+00 1enj 138 -16.36 -7.46 1.68e+00 1f07A 321 -16.12 -7.22 2.06e+00 1x9mA 698 -17.05 -7.21 2.10e+00 1wpgA 994 -18.30 -7.08 2.34e+00 1urqA 63 -16.30 -6.85 2.84e+00 1ovnA 248 -15.61 -6.60 3.55e+00 1su4A 994 -17.34 -6.34 4.46e+00 1zvdA 380 -14.84 -6.26 4.77e+00 1h6hA 143 -14.27 -6.23 4.90e+00 1ii6A 368 -14.14 -6.05 5.74e+00 1tueB 218 -14.69 -6.04 5.83e+00 1jeyB 565 -14.58 -6.03 5.86e+00 1ll0A 339 -14.60 -6.01 5.95e+00 1wwpA 119 -17.57 -6.01 5.97e+00 1f88A 348 -16.42 -6.00 6.02e+00 1jeqB 565 -14.52 -6.00 6.05e+00 1bx4A 345 -14.37 -5.95 6.29e+00 1k0nA 241 -15.21 -5.93 6.41e+00 1qrqA 325 -14.59 -5.92 6.46e+00 1t7pA 698 -15.63 -5.83 6.99e+00 1xc0A 33 -13.36 -5.66 8.20e+00 1t0qA 498 -15.04 -5.62 8.49e+00 1dfoA 417 -14.94 -5.62 8.51e+00 1tgoA 773 -15.10 -5.60 8.65e+00 1s5lX 50 -16.12 -5.57 8.87e+00 1vk9A 151 -13.95 -5.54 9.16e+00 1v9mA 323 -14.63 -5.45 9.93e+00 1rwtA 232 -15.57 -5.43 1.02e+01 1n2sA 299 -13.45 -5.38 1.06e+01 1ebbA 202 -14.29 -5.38 1.07e+01 1qhtA 775 -14.65 -5.37 1.07e+01 3pbgA 468 -13.99 -5.34 1.11e+01 1ll2A 333 -13.85 -5.31 1.13e+01 1b4fA 82 -14.22 -5.28 1.16e+01 1pbgA 468 -13.96 -5.28 1.16e+01 1h2eA 207 -14.22 -5.28 1.17e+01 1b4fG 82 -14.11 -5.26 1.18e+01 1rzl 91 -14.19 -5.26 1.18e+01 1m2eA 135 -12.84 -5.25 1.20e+01 2bifA 469 -14.35 -5.23 1.22e+01 1f0mA 82 -14.07 -5.22 1.23e+01 1zsyA 357 -13.38 -5.20 1.25e+01 1q52A 314 -15.42 -5.18 1.28e+01 1bif 469 -14.25 -5.18 1.28e+01 1z83A 196 -13.53 -5.01 1.51e+01 1de5A 426 -14.02 -4.94 1.60e+01 1yaxA 153 -12.66 -4.93 1.61e+01 1f3iA 481 -13.98 -4.91 1.64e+01 2a3qA 170 -14.47 -4.90 1.67e+01 1yw0A 276 -15.67 -4.89 1.67e+01 1r12A 258 -13.16 -4.84 1.77e+01 1ufbA 127 -14.11 -4.83 1.78e+01 1yydA 357 -13.62 -4.77 1.88e+01 1mn1 357 -13.62 -4.76 1.90e+01 1fk5A 93 -14.08 -4.76 1.91e+01 1mzm 93 -14.08 -4.76 1.91e+01 1iv8A 720 -14.24 -4.75 1.92e+01 1mnp 357 -13.62 -4.74 1.94e+01 1sgg 75 -13.64 -4.74 1.94e+01 1ezvF 125 -14.30 -4.74 1.95e+01 1a8rA 221 -12.99 -4.73 1.96e+01 3bifA 468 -13.88 -4.73 1.96e+01 1y3nA 490 -14.10 -4.69 2.03e+01 1j5eB 256 -12.98 -4.69 2.03e+01 1tv9A 335 -13.44 -4.63 2.15e+01 1xkpA 246 -14.19 -4.62 2.17e+01 1a17 166 -13.95 -4.61 2.20e+01 2c5uA 375 -13.05 -4.60 2.21e+01 1x3kA 152 -14.41 -4.60 2.22e+01 1wucA 250 -13.14 -4.59 2.24e+01 1kb9G 125 -14.14 -4.58 2.26e+01 1bc5A 269 -13.07 -4.58 2.27e+01 1tdpA 111 -13.38 -4.57 2.28e+01 1me4A 215 -13.30 -4.56 2.31e+01 1k0mA 241 -15.27 -4.56 2.32e+01 1wyuB 474 -13.94 -4.55 2.34e+01 1af7 274 -13.03 -4.53 2.38e+01 1f2aA 215 -13.30 -4.52 2.41e+01 1abmA 198 -13.11 -4.47 2.52e+01 1qazA 351 -15.44 -4.47 2.53e+01 1de6A 426 -13.39 -4.44 2.60e+01 1n4oA 276 -14.48 -4.43 2.62e+01 1fbtA 190 -13.05 -4.42 2.64e+01 1nh1A 330 -13.49 -4.40 2.69e+01 1oya 400 -13.10 -4.39 2.71e+01 1o7eA 276 -14.00 -4.38 2.75e+01 2lhb 149 -13.82 -4.38 2.75e+01 1me3A 215 -13.04 -4.37 2.77e+01 1uelB 48 -11.88 -4.34 2.86e+01 1jmsA 381 -13.96 -4.34 2.87e+01 1bpyA 335 -13.08 -4.34 2.87e+01 1cy5A 97 -13.36 -4.34 2.87e+01 1oyc 400 -13.12 -4.33 2.90e+01 1l9hA 349 -14.72 -4.30 2.98e+01 1afh 93 -13.74 -4.30 2.98e+01 1lj8A 493 -12.91 -4.29 3.00e+01 1yruB 74 -13.31 -4.28 3.04e+01 1b4cA 92 -14.32 -4.28 3.05e+01 1to6A 371 -13.03 -4.27 3.05e+01 1yrlA 491 -15.59 -4.27 3.07e+01 2kauA 100 -14.17 -4.26 3.10e+01 1xrdA 52 -14.27 -4.25 3.12e+01 1ash 150 -13.62 -4.25 3.12e+01 1w9yA 319 -12.82 -4.24 3.16e+01 1aim 215 -13.30 -4.23 3.19e+01 1d8wA 426 -13.26 -4.22 3.22e+01 1k3kA 158 -14.76 -4.21 3.24e+01 1hnnA 282 -12.39 -4.21 3.26e+01 1vflA 356 -14.37 -4.21 3.27e+01 1ejxA 100 -14.16 -4.20 3.30e+01 1fwcA 100 -14.16 -4.20 3.30e+01 1r0pA 312 -13.08 -4.19 3.31e+01 1r30A 369 -13.50 -4.18 3.35e+01 1tbfA 347 -13.73 -4.16 3.42e+01 1xfxO 149 -12.88 -4.12 3.56e+01 1qgtA 149 -13.18 -4.10 3.62e+01 2ahjA 206 -13.55 -4.10 3.62e+01 1qqcA 773 -13.58 -4.08 3.69e+01 1ulyA 192 -13.59 -4.08 3.72e+01 2a9uA 144 -13.84 -4.07 3.75e+01 2cz1A 206 -13.53 -4.06 3.77e+01 1dceA 567 -13.61 -4.06 3.79e+01 1a9cA 221 -12.55 -4.06 3.79e+01 1usgA 346 -12.88 -4.05 3.83e+01 1kdxB 28 -11.51 -4.04 3.84e+01 2ygsA 92 -12.85 -4.04 3.87e+01 1kb0A 677 -12.12 -4.02 3.92e+01 2bg1A 494 -13.00 -4.02 3.94e+01