% 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.YEL022W.t2k-100-30-CB_burial_14_7 Host: farm16 Tue Dec 28 22:19:12 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YEL0/YEL022W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/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 YEL022W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL022W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 11147 sequences, 2640567 residues, 1460 nodes, 1999.99 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(=1.2869) * Reverse)^tau(=0.8429))) % 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 1r8mE 203 -287.59 -270.20 6.16e-57 1r8sE 203 -282.70 -266.25 3.41e-56 1ku1A 230 -284.37 -265.34 5.06e-56 1pbv 195 -278.61 -261.53 2.65e-55 1xszA 356 -210.92 -192.76 5.16e-42 1nw8A 319 -31.82 -12.97 2.35e-01 1eg2A 319 -31.67 -12.83 2.59e-01 1es9A 232 -25.79 -11.10 8.78e-01 1ibrB 462 -31.00 -10.58 1.28e+00 1xg9A 260 -28.72 -10.54 1.31e+00 1qgrA 876 -49.97 -10.54 1.31e+00 1jplA 171 -26.91 -10.40 1.45e+00 1wab 232 -24.68 -10.17 1.72e+00 1ad3A 452 -31.86 -10.04 1.89e+00 1qbkB 890 -47.02 -9.80 2.24e+00 1fyhA 258 -34.29 -9.80 2.24e+00 1gw5A 621 -38.03 -9.07 3.82e+00 1nfiA 301 -26.07 -9.02 3.96e+00 1gw5B 591 -44.95 -8.86 4.48e+00 1lt8A 406 -28.27 -8.84 4.54e+00 1nc5A 373 -24.51 -8.54 5.68e+00 1bt3A 345 -24.21 -8.47 5.99e+00 1oj6A 151 -22.46 -8.45 6.07e+00 1w36C 1122 -36.58 -8.39 6.35e+00 1nfiC 301 -25.39 -8.23 7.14e+00 1korA 400 -26.76 -8.11 7.80e+00 1mhqA 148 -23.03 -7.90 9.12e+00 1owcA 427 -27.26 -7.89 9.19e+00 1i1qA 520 -24.31 -7.89 9.20e+00 1rkpA 326 -23.49 -7.83 9.66e+00 1q1fA 151 -21.49 -7.69 1.07e+01 1np3A 338 -31.00 -7.65 1.11e+01 1gpjA 404 -26.54 -7.55 1.19e+01 2dpmA 284 -24.62 -7.54 1.20e+01 1tiqA 180 -22.86 -7.36 1.38e+01 1jrrA 382 -22.69 -7.30 1.45e+01 1a0cA 438 -31.25 -7.27 1.48e+01 1k3pA 426 -26.24 -7.24 1.51e+01 1xqoA 256 -20.08 -7.20 1.56e+01 1jx2B 315 -24.76 -6.99 1.82e+01 1vzoA 355 -23.10 -6.85 2.04e+01 1fgyA 127 -21.69 -6.84 2.04e+01 1eqnA 321 -24.71 -6.80 2.12e+01 1v9mA 323 -20.30 -6.67 2.34e+01 1ekbB 235 -18.43 -6.66 2.36e+01 1h38D 883 -38.92 -6.65 2.37e+01 1dd9A 338 -25.50 -6.60 2.46e+01 1ddeA 338 -25.62 -6.57 2.53e+01 1jwyB 315 -24.56 -6.48 2.70e+01 1vorS 100 -28.25 -6.39 2.91e+01 1upkA 341 -26.54 -6.38 2.93e+01 1rw2A 152 -26.03 -6.37 2.96e+01 1vhyA 257 -20.60 -6.36 2.98e+01 1r5zA 323 -19.78 -6.35 3.01e+01 1fps 348 -24.43 -6.32 3.07e+01 1ku2A 241 -24.39 -6.25 3.24e+01 1h38B 883 -38.54 -6.19 3.38e+01 1q52A 314 -23.23 -6.11 3.61e+01 1onrA 316 -21.45 -6.11 3.62e+01 1dl2A 511 -22.61 -6.10 3.65e+01 1jeqA 609 -39.17 -6.10 3.66e+01 1xpcA 248 -20.79 -6.08 3.71e+01 1efuB 282 -24.07 -6.01 3.92e+01 1r6uA 437 -29.56 -6.00 3.94e+01