% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 06/01/06_09:03:53 % (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.YGR224W.t2k-100-30-CB_burial_14_7 Host: farm11-10.kilokluster.ucsc.edu Fri Oct 6 08:44:21 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR224W % --------------------------------------------------------------------- % 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 YGR224W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR224W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 15583 sequences, 3659059 residues, 614 nodes, 1033.35 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(=0.9080) * Reverse)^tau(=0.8695))) % 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 1pw4A 451 -181.63 -154.18 1.38e-28 2gfpA 375 -160.65 -141.87 2.31e-26 1pv6A 417 -87.28 -64.22 1.39e-11 2cfqA 417 -86.56 -62.69 2.84e-11 1vl6A 388 -56.62 -13.95 1.24e+00 2a65A 519 -37.38 -12.56 2.73e+00 1w5qA 337 -39.47 -11.54 4.92e+00 1gzgA 337 -39.28 -11.53 4.95e+00 1w5nA 337 -38.25 -11.43 5.25e+00 2iufA 688 -70.63 -11.40 5.35e+00 1kgnA 329 -53.31 -11.32 5.58e+00 2c2aA 258 -49.13 -11.00 6.74e+00 1b4kA 337 -39.10 -11.00 6.75e+00 1b5sA 242 -35.81 -10.93 7.01e+00 1eysH 259 -39.63 -10.62 8.42e+00 1qwlA 505 -90.48 -10.54 8.83e+00 1kimA 366 -25.75 -10.53 8.86e+00 2cm2A 304 -49.48 -10.27 1.04e+01 1qhiA 366 -25.57 -10.16 1.10e+01 1sczA 233 -32.62 -10.14 1.12e+01 1sesA 421 -50.00 -9.94 1.25e+01 2ki5A 366 -25.20 -9.86 1.32e+01 1reqD 637 -70.79 -9.59 1.54e+01 3vtk 343 -25.34 -9.56 1.57e+01 1d8iA 311 -51.20 -9.53 1.61e+01 1qi9A 556 -53.73 -9.49 1.64e+01 1sy7A 715 -82.60 -9.46 1.67e+01 2hb6A 491 -47.03 -9.43 1.70e+01 7reqB 637 -70.57 -9.43 1.70e+01 1wgzA 510 -56.76 -9.42 1.71e+01 1kinA 366 -25.64 -9.39 1.74e+01 2hc9A 491 -46.99 -9.37 1.76e+01 1e2o 233 -31.25 -9.35 1.78e+01 1eulA 994 -99.34 -9.34 1.79e+01 2if1 126 -38.66 -9.34 1.79e+01 1tbgA 340 -37.95 -9.25 1.90e+01 2c82A 413 -23.48 -9.20 1.95e+01 1k87A 669 -62.00 -9.18 1.97e+01 1reqB 637 -70.41 -9.17 1.98e+01 1wpgA 994 -100.06 -9.12 2.04e+01 1d8hA 311 -50.50 -9.04 2.15e+01 1cjl 312 -51.92 -8.99 2.21e+01 1wchA 315 -39.72 -8.96 2.25e+01 2bm8A 236 -38.30 -8.94 2.28e+01 1a4eA 488 -68.15 -8.90 2.33e+01 1g6oA 330 -47.28 -8.87 2.37e+01 1gotB 340 -37.69 -8.87 2.38e+01 1cs8A 316 -52.94 -8.87 2.38e+01 1a5y 330 -48.44 -8.83 2.44e+01 1e2kA 331 -23.48 -8.80 2.48e+01 2bcjB 340 -37.93 -8.80 2.49e+01 1o4sA 389 -49.14 -8.79 2.49e+01 1jjyA 636 -52.40 -8.78 2.51e+01 1a0rB 340 -37.38 -8.75 2.56e+01 1dceA 567 -69.16 -8.60 2.79e+01 2bzpA 226 -40.13 -8.58 2.83e+01 2gnxA 365 -29.49 -8.52 2.94e+01 1sr9A 644 -73.60 -8.48 3.00e+01 1p2zA 968 -95.98 -8.48 3.01e+01 5reqA 727 -77.97 -8.46 3.04e+01 1p30A 952 -101.49 -8.41 3.14e+01 1reqA 727 -78.30 -8.37 3.21e+01 1mhyB 395 -46.84 -8.36 3.23e+01 1aym1 285 -42.73 -8.36 3.23e+01 1akaA 401 -47.01 -8.33 3.29e+01 1yymG 313 -40.93 -8.32 3.31e+01 1dx5I 118 -34.02 -8.24 3.48e+01 1bh5A 183 -37.57 -8.24 3.48e+01 1ap8 213 -42.39 -8.23 3.50e+01 1b4eA 323 -37.45 -8.23 3.51e+01 1ruxA 951 -100.96 -8.22 3.51e+01 1tmxA 293 -39.79 -8.22 3.53e+01 1ohgA 282 -33.78 -8.21 3.54e+01 7aatA 401 -47.32 -8.19 3.58e+01 1zodA 433 -29.74 -8.17 3.62e+01 1su4A 994 -98.89 -8.17 3.63e+01 1euvA 221 -40.00 -8.17 3.63e+01 1th0A 226 -37.06 -8.16 3.66e+01 1ek9A 428 -44.05 -8.15 3.68e+01 1ireA 204 -39.96 -8.09 3.81e+01 2hnp 321 -46.69 -8.05 3.90e+01 1ugpA 203 -40.38 -8.01 3.99e+01 2bolA 314 -55.21 -8.01 4.00e+01