% 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. % --------------------------------------------------------------------- % str2foo.1.YDL114W-A.t2k-100-30-str2 Host: farm05 Mon Nov 29 12:23:17 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDL1/YDL114W-A % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s % % 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 YDL114W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDL114W-A.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 38 nodes, 43.19 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(=3.9070) * Reverse)^tau(=0.6827))) % 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 1d1nA 99 -15.11 -7.09 6.87e-01 3ait 74 -13.62 -6.54 1.15e+00 1ok0A 74 -13.24 -6.48 1.21e+00 1hoe 74 -13.20 -6.45 1.25e+00 1jhsA 188 -12.79 -5.92 2.09e+00 1eq6A 189 -12.52 -5.66 2.71e+00 2ait 74 -11.89 -5.22 4.23e+00 8fabA 212 -12.44 -4.97 5.47e+00 1jiwI 106 -11.81 -4.93 5.72e+00 1quqB 121 -12.15 -4.90 5.90e+00 1rzfL 213 -12.47 -4.84 6.24e+00 1bjmA 216 -12.47 -4.71 7.17e+00 1bfd 528 -11.17 -4.38 1.03e+01 1k8wA 327 -11.35 -4.36 1.04e+01 1hcnA 92 -11.81 -4.35 1.06e+01 1dvfD 120 -11.47 -4.28 1.14e+01 1dz7A 92 -10.68 -4.22 1.22e+01 1lylA 504 -11.07 -3.92 1.70e+01 1iakA 199 -12.07 -3.90 1.73e+01 1ssfA 156 -10.69 -3.90 1.74e+01 1eueA 86 -10.19 -3.86 1.81e+01 1gcpA 70 -10.52 -3.86 1.83e+01 1qo3C 137 -11.80 -3.84 1.86e+01 1fniA 223 -11.13 -3.81 1.93e+01 1s83A 223 -11.06 -3.77 2.02e+01 1mctA 223 -11.11 -3.76 2.03e+01 1h9hE 223 -11.10 -3.75 2.06e+01 1gcqC 70 -10.58 -3.71 2.16e+01 1pht 85 -10.37 -3.68 2.24e+01 1k1zA 78 -10.22 -3.66 2.29e+01 1ujqA 305 -9.59 -3.64 2.35e+01 1e1oA 504 -10.88 -3.63 2.36e+01 1s3jA 155 -9.39 -3.63 2.37e+01 1ny72 369 -11.52 -3.57 2.54e+01 1eajA 126 -10.47 -3.54 2.62e+01 1f5wA 126 -10.47 -3.54 2.62e+01 1h4wA 224 -10.83 -3.51 2.71e+01 1xfoA 357 -10.28 -3.51 2.73e+01 1hfi 62 -10.21 -3.50 2.74e+01 1xebA 150 -9.78 -3.43 2.99e+01 1mo7A 213 -9.84 -3.41 3.05e+01 1lj0A 92 -9.58 -3.32 3.39e+01 1h6kX 97 -10.03 -3.31 3.42e+01 1ogqA 313 -10.27 -3.30 3.46e+01 1a0jA 223 -10.44 -3.30 3.48e+01 1nra 63 -11.22 -3.29 3.52e+01 1h6kZ 98 -10.00 -3.28 3.57e+01 1zncA 266 -10.27 -3.27 3.58e+01 1juvA 193 -10.18 -3.27 3.59e+01 1g5cA 170 -9.58 -3.26 3.66e+01 1so7A 382 -12.99 -3.19 3.93e+01