% 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.YGR032W.t2k-100-30-CB_burial_14_7 Host: farm08 Thu Nov 18 03:16:26 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR032W % --------------------------------------------------------------------- % 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 YGR032W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR032W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10772 sequences, 2550165 residues, 1896 nodes, 2481.91 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(=1.6535) * Reverse)^tau(=0.7216))) % 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 1qvjA 292 -27.53 -11.60 2.34e+00 1ovnA 248 -27.00 -11.44 2.55e+00 1ehkA 562 -34.13 -11.36 2.65e+00 1jmoA 480 -32.75 -11.23 2.85e+00 1q33A 292 -27.05 -11.12 3.02e+00 1gln 468 -29.25 -10.82 3.54e+00 1kmmA 424 -28.36 -10.53 4.13e+00 2thiA 379 -25.31 -10.19 4.97e+00 1gm5A 780 -30.38 -10.17 5.02e+00 1g59A 468 -28.61 -9.85 5.98e+00 1j09A 468 -28.83 -9.81 6.10e+00 1rh5B 74 -29.58 -9.47 7.37e+00 3thiA 371 -24.35 -9.25 8.32e+00 1jcqA 382 -27.79 -9.09 9.11e+00 1gt8A 1025 -46.22 -9.05 9.34e+00 1gthD 1025 -45.88 -9.01 9.50e+00 1m1jA 491 -46.65 -8.98 9.69e+00 1gthB 1025 -46.09 -8.97 9.76e+00 1h7wA 1025 -46.23 -8.91 1.01e+01 1h7wB 1025 -46.05 -8.88 1.03e+01 1fqiA 147 -24.87 -8.86 1.04e+01 1gt8B 1025 -45.69 -8.83 1.05e+01 1gthA 1025 -45.79 -8.83 1.06e+01 1h7wD 1025 -46.12 -8.82 1.06e+01 1gteA 1025 -46.03 -8.74 1.11e+01 1gthC 1025 -45.96 -8.71 1.13e+01 1gt8D 1025 -45.98 -8.70 1.14e+01 1h7xC 1025 -45.58 -8.59 1.21e+01 1tn6A 382 -27.08 -8.59 1.21e+01 1h7xA 1025 -45.57 -8.56 1.23e+01 1dlc 584 -25.87 -8.53 1.25e+01 1ld8A 382 -27.21 -8.52 1.25e+01 1httA 423 -27.44 -8.51 1.27e+01 1h7xD 1025 -45.56 -8.50 1.27e+01 1gteD 1025 -45.88 -8.44 1.32e+01 1ap8 213 -26.09 -8.41 1.34e+01 1ft1A 377 -26.49 -8.40 1.34e+01 1kmnD 424 -25.99 -8.39 1.35e+01 1h7xB 1025 -45.01 -8.23 1.49e+01 1mnmA 100 -27.74 -8.16 1.55e+01 1gt8C 1025 -44.73 -8.09 1.61e+01 7reqB 637 -25.91 -7.85 1.85e+01 1qbqA 333 -25.83 -7.58 2.17e+01 1jcrA 377 -26.45 -7.41 2.40e+01 1qhdA 398 -21.34 -7.36 2.46e+01 1ux5A 411 -31.42 -7.19 2.73e+01 1ichA 112 -21.52 -7.18 2.75e+01 1d8dA 377 -26.14 -7.13 2.82e+01 1l9hA 349 -26.32 -7.12 2.84e+01 1gjwA 637 -30.72 -6.97 3.12e+01 1a76 326 -25.84 -6.85 3.34e+01 1fz1C 389 -26.84 -6.84 3.36e+01 1mg7A 417 -21.73 -6.77 3.52e+01 1f88A 348 -25.62 -6.75 3.56e+01 1clqA 903 -33.04 -6.66 3.75e+01 1hzxA 349 -25.88 -6.64 3.81e+01 1ez0A 510 -20.41 -6.59 3.92e+01