% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % dsspfoo.1.YGR018C.t2k-100-30-dssp-ebghstl Host: cc49 Tue Nov 12 04:24:47 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR018C % --------------------------------------------------------------------- % 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 ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR018C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR018C.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 110 nodes, 73.86 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 (=7316) sequences: % N / (1 + exp(-(lambda(=2.2090) * Reverse)^tau(=0.7718))) % 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 1gosA 520 -34.41 -11.38 4.30e-02 1ac6A 110 -27.24 -9.00 3.16e-01 1bcpC 199 -27.20 -8.26 6.00e-01 3gcb 470 -28.20 -7.60 1.09e+00 1gcb 454 -28.02 -7.48 1.20e+00 1a6r 471 -27.80 -7.20 1.55e+00 1jrhI 108 -24.95 -6.44 3.10e+00 1dnlA 199 -24.98 -6.22 3.84e+00 1jm6A 407 -27.09 -6.02 4.60e+00 1ahm 129 -26.34 -5.93 5.02e+00 1g79A 218 -24.84 -5.86 5.36e+00 3rp2A 224 -26.25 -5.78 5.82e+00 1qa1A 554 -27.83 -5.77 5.87e+00 1qq1A 559 -27.77 -5.62 6.77e+00 1fg9C 245 -26.29 -5.54 7.27e+00 1hzgA 295 -25.28 -5.45 7.97e+00 1tsp 559 -27.51 -5.44 8.06e+00 1hq0A 295 -25.27 -5.43 8.11e+00 1a3qA 285 -26.38 -5.39 8.42e+00 1fyhB 229 -25.90 -5.39 8.43e+00 1fm0E 150 -22.97 -5.33 8.94e+00 1fmaE 150 -22.97 -5.32 8.98e+00 1bomB 28 -20.47 -5.31 9.11e+00 1jevA 517 -26.60 -5.29 9.31e+00 1rl2A 137 -23.24 -5.11 1.11e+01 1cleA 534 -27.24 -5.10 1.11e+01 2hlcA 230 -28.04 -5.10 1.12e+01 1lcyA 325 -26.35 -5.08 1.14e+01 1ac5 483 -27.98 -4.98 1.26e+01 2olbA 517 -26.31 -4.96 1.29e+01 1theA 260 -25.29 -4.89 1.38e+01 1hylA 230 -27.01 -4.77 1.55e+01 1crl 534 -26.85 -4.73 1.62e+01 1k5jA 124 -24.12 -4.70 1.67e+01 1tyu 543 -26.44 -4.58 1.87e+01 1erjA 393 -25.42 -4.52 1.98e+01 1sly 618 -24.87 -4.52 2.00e+01 1eylA 186 -25.39 -4.51 2.01e+01 1icfB 42 -20.09 -4.38 2.28e+01 1bvoA 175 -24.15 -4.38 2.29e+01 1qsaA 618 -24.66 -4.34 2.39e+01 1hgeA 328 -24.74 -4.29 2.50e+01 1jrmA 104 -22.65 -4.28 2.52e+01 1f42A 306 -26.34 -4.26 2.58e+01 1fbr 93 -22.19 -4.26 2.59e+01 1jrkA 156 -22.94 -4.24 2.63e+01 1tib 269 -24.37 -4.22 2.70e+01 1jetA 517 -25.22 -4.21 2.73e+01 1sgt 223 -24.11 -4.21 2.74e+01 1theB 260 -24.57 -4.19 2.77e+01 2vil 126 -22.38 -4.14 2.93e+01 2viuA 328 -24.56 -4.12 2.98e+01 1k2eA 156 -23.00 -4.10 3.06e+01 1bypA 99 -21.92 -4.09 3.07e+01 2vik 126 -22.32 -4.09 3.08e+01 1k26A 156 -22.94 -4.05 3.21e+01 1nfkA 325 -26.13 -4.05 3.22e+01 1ueaB 184 -23.70 -4.04 3.23e+01 2ifeA 100 -21.12 -4.01 3.34e+01 1ci0A 228 -23.69 -3.99 3.41e+01 1h8lA 380 -24.20 -3.98 3.44e+01 1jfmA 174 -23.02 -3.96 3.52e+01 1f5mB 180 -23.30 -3.95 3.57e+01 1f5mA 180 -23.27 -3.91 3.71e+01 2mjpA 193 -23.04 -3.88 3.82e+01 1qmuA 380 -23.99 -3.87 3.88e+01 1zfjA 491 -24.50 -3.86 3.89e+01