% 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.YGR236C.t2k-100-30-stride-ebghtl Host: farm16.cse.ucsc.edu Fri Mar 3 08:49:57 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.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 YGR236C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR236C.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14381 sequences, 3373755 residues, 96 nodes, 159.11 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(=2.3266) * Reverse)^tau(=0.7437))) % 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 1zvdA 380 -18.05 -9.15 6.57e-01 1yaxA 153 -16.44 -8.16 1.46e+00 1m6dA 214 -15.71 -7.20 3.21e+00 1r12A 258 -15.56 -7.17 3.30e+00 1nt4A 391 -17.24 -7.04 3.69e+00 1n2sA 299 -15.38 -7.04 3.70e+00 1lbeA 258 -15.44 -7.02 3.75e+00 1r5zA 323 -16.18 -6.79 4.57e+00 1mnp 357 -15.31 -6.65 5.16e+00 1yydA 357 -15.31 -6.64 5.19e+00 1u04A 771 -15.39 -6.47 6.00e+00 1mn1 357 -15.07 -6.43 6.23e+00 1wpgA 994 -16.76 -6.31 6.87e+00 1x9mA 698 -16.25 -6.24 7.35e+00 1enj 138 -15.51 -6.07 8.50e+00 1su4A 994 -16.95 -6.05 8.62e+00 1tueB 218 -14.48 -6.02 8.86e+00 1lfpA 249 -14.91 -6.02 8.90e+00 2bykA 140 -14.99 -5.91 9.80e+00 1xc0A 33 -14.55 -5.88 1.01e+01 1s5lX 50 -16.55 -5.85 1.04e+01 1eni 138 -15.14 -5.82 1.06e+01 1ll2A 333 -14.42 -5.79 1.09e+01 1enk 138 -15.06 -5.70 1.18e+01 1z83A 196 -14.33 -5.67 1.21e+01 2end 138 -14.97 -5.60 1.29e+01 1f07A 321 -14.75 -5.52 1.39e+01 1qqhA 144 -12.95 -5.51 1.40e+01 1ws6A 171 -13.45 -5.48 1.44e+01 1vasA 137 -14.52 -5.43 1.50e+01 2bifA 469 -14.42 -5.41 1.53e+01 1exbA 332 -14.16 -5.39 1.56e+01 1bg6 359 -14.56 -5.35 1.61e+01 1ash 150 -14.46 -5.28 1.73e+01 1jeqB 565 -14.35 -5.26 1.74e+01 1bx4A 345 -13.88 -5.26 1.75e+01 1fbtA 190 -13.97 -5.25 1.76e+01 1zsxA 347 -14.11 -5.23 1.81e+01 3pbgA 468 -14.11 -5.21 1.83e+01 1a17 166 -14.20 -5.17 1.90e+01 2cz1A 206 -13.83 -5.14 1.95e+01 2ahjA 206 -13.79 -5.14 1.96e+01 1jeyB 565 -14.32 -5.11 2.01e+01 1ll0A 339 -14.14 -5.08 2.06e+01 1f88A 348 -15.90 -5.08 2.07e+01 2ew2A 316 -14.12 -5.06 2.10e+01 1pbgA 468 -14.06 -5.06 2.10e+01 1o2dA 371 -16.65 -5.01 2.19e+01 1yw0A 276 -15.58 -4.99 2.25e+01 1dceA 567 -14.18 -4.98 2.26e+01 1binB 143 -13.68 -4.93 2.36e+01 1lfdA 87 -12.72 -4.91 2.41e+01 3bifA 468 -14.03 -4.90 2.43e+01 1t7pA 698 -14.83 -4.90 2.44e+01 1gpmA 525 -13.28 -4.86 2.52e+01 1ehkB 168 -13.52 -4.83 2.61e+01 1t0qA 498 -14.01 -4.82 2.62e+01 1u5tA 233 -13.91 -4.78 2.74e+01 1o51A 114 -12.56 -4.76 2.79e+01 1oyc 400 -13.47 -4.74 2.84e+01 1mioA 534 -13.71 -4.72 2.87e+01 1ap6A 198 -13.25 -4.72 2.87e+01 1oyb 400 -13.47 -4.72 2.87e+01 1ak0 270 -13.89 -4.72 2.89e+01 1wwpA 119 -15.59 -4.71 2.90e+01 1abmA 198 -13.25 -4.71 2.91e+01 1ii6A 368 -13.32 -4.71 2.91e+01 1lxdA 100 -12.34 -4.71 2.92e+01 1oya 400 -13.47 -4.70 2.93e+01 1pl4A 198 -13.25 -4.70 2.93e+01 1rwtA 232 -14.66 -4.66 3.04e+01 1rzl 91 -13.47 -4.66 3.04e+01 1ahjA 207 -13.77 -4.66 3.06e+01 1le6A 123 -12.67 -4.63 3.12e+01 2ahjC 206 -13.68 -4.59 3.24e+01 1bif 469 -13.57 -4.59 3.25e+01 1ovnA 248 -13.72 -4.58 3.30e+01 1yrlA 491 -15.55 -4.57 3.33e+01 1zsyA 357 -13.35 -4.56 3.34e+01 3adk 195 -13.35 -4.54 3.43e+01 1z3xA 238 -14.42 -4.53 3.44e+01 1j8mF 297 -14.75 -4.51 3.51e+01 1qrqA 325 -13.23 -4.51 3.53e+01 1lj8A 493 -13.46 -4.51 3.53e+01 1j8yF 297 -14.75 -4.50 3.53e+01 1v9mA 323 -13.85 -4.47 3.64e+01 1xrdA 52 -14.58 -4.46 3.68e+01 1cxpC 466 -16.31 -4.43 3.77e+01 1eulA 994 -14.97 -4.39 3.94e+01 1b4fG 82 -12.82 -4.39 3.95e+01 1m2eA 135 -12.19 -4.38 3.98e+01