% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YCL048W-A.t2k-100-30-dssp-ehl2 Host: farm11.cse.ucsc.edu Fri Mar 3 08:21:27 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YCL0/YCL048W-A % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.dssps % % 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 YCL048W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YCL048W-A.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14381 sequences, 3373755 residues, 80 nodes, 131.68 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(=2.5966) * Reverse)^tau(=0.7296))) % 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 1jb0K 83 -14.16 -5.64 9.17e+00 1c17M 177 -14.36 -5.57 9.83e+00 1yp2A 451 -14.15 -5.31 1.24e+01 1ds4A 292 -14.12 -5.30 1.25e+01 1thjA 214 -14.71 -5.25 1.31e+01 1ccg 291 -14.05 -5.25 1.31e+01 1dseA 292 -14.57 -5.20 1.38e+01 1zxmA 400 -14.43 -5.03 1.62e+01 1qreA 247 -15.18 -5.00 1.66e+01 1v54K 56 -13.70 -4.97 1.72e+01 2occK 56 -13.70 -4.97 1.72e+01 1u6mA 199 -13.03 -4.91 1.82e+01 1q3jA 36 -12.51 -4.81 2.00e+01 1vprA 374 -14.45 -4.80 2.01e+01 1sh1 48 -12.42 -4.79 2.03e+01 1nqcA 217 -13.22 -4.79 2.04e+01 1dtoA 221 -12.43 -4.74 2.12e+01 1n13A 52 -12.58 -4.63 2.37e+01 1n0xL 215 -12.44 -4.63 2.38e+01 1um5L 219 -12.56 -4.59 2.46e+01 1hi2A 135 -12.90 -4.45 2.82e+01 1aw9 216 -12.71 -4.45 2.83e+01 1ad9A 219 -13.65 -4.37 3.05e+01 2aj2A 208 -12.92 -4.36 3.10e+01 1c5cL 214 -12.30 -4.35 3.12e+01 1rwzA 245 -12.50 -4.34 3.13e+01 1bo4B 168 -12.17 -4.31 3.24e+01 1l7iL 214 -12.30 -4.28 3.33e+01 1gdhA 320 -13.28 -4.26 3.41e+01 1ngzA 213 -12.59 -4.21 3.57e+01 1sa3A 262 -12.16 -4.20 3.59e+01 1nar 290 -12.71 -4.20 3.60e+01 1n35A 1267 -13.50 -4.18 3.67e+01 1axsA 211 -12.46 -4.18 3.68e+01 1jb1A 205 -13.16 -4.18 3.69e+01 1i7nA 309 -12.23 -4.11 3.94e+01 1bw0A 416 -13.10 -4.10 3.98e+01