% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YDL013W.t2k-100-30-dssp-ehl2 Host: cc65 Mon Nov 11 16:54:47 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDL0/YDL013W % --------------------------------------------------------------------- % 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 YDL013W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDL013W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 620 nodes, 420.91 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 (=7316) sequences: % N / (1 + exp(-(lambda(=1.0403) * Reverse)^tau(=0.8502))) % 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 1bpoA 494 -46.21 -19.24 2.07e-02 1ezvC 385 -41.23 -11.02 2.56e+00 1kyoC 385 -41.09 -10.78 2.98e+00 1e6yA 569 -37.16 -10.51 3.51e+00 1knyA 253 -34.88 -10.02 4.75e+00 1b3uA 588 -47.27 -9.78 5.51e+00 1gaxA 862 -41.96 -9.72 5.74e+00 1k8kG 151 -32.71 -9.56 6.35e+00 1h9dB 134 -30.78 -9.50 6.59e+00 2gd1O 334 -32.95 -9.19 8.01e+00 1qfcA 306 -33.54 -9.07 8.63e+00 1e50B 134 -29.78 -9.04 8.78e+00 1jm7A 112 -30.04 -8.87 9.78e+00 1cqzA 554 -34.67 -8.83 1.00e+01 1rdg 53 -27.14 -8.76 1.05e+01 1gd1O 334 -32.54 -8.67 1.11e+01 1cr6B 554 -34.04 -8.48 1.26e+01 1bxlA 181 -35.77 -8.47 1.26e+01 1qcrC 378 -35.63 -8.42 1.31e+01 2jhbA 143 -29.07 -8.40 1.32e+01 1hqcA 324 -34.39 -8.26 1.45e+01 1dn1B 267 -43.21 -8.25 1.45e+01 1f6fA 199 -36.68 -8.14 1.55e+01 1i4lA 224 -42.04 -8.11 1.59e+01 1jlxA 304 -33.05 -8.08 1.62e+01 1hdhA 536 -35.11 -8.05 1.65e+01 1jk0A 419 -39.92 -8.02 1.68e+01 1f16A 192 -35.02 -8.00 1.70e+01 1ek1A 554 -32.85 -7.96 1.74e+01 1jlyA 304 -32.60 -7.94 1.77e+01 1kgnA 329 -42.66 -7.93 1.79e+01 1dkgD 383 -33.38 -7.90 1.82e+01 1f0xA 571 -32.81 -7.72 2.04e+01 1j5vA 351 -32.24 -7.68 2.10e+01 1qs2A 401 -37.06 -7.66 2.12e+01 1g41A 444 -35.13 -7.58 2.24e+01 1g5aA 628 -37.24 -7.43 2.46e+01 1h99A 224 -36.90 -7.42 2.48e+01 1dvpA 220 -34.56 -7.38 2.55e+01 1qklA 127 -29.39 -7.27 2.74e+01 3pflA 759 -37.59 -7.21 2.84e+01 1g25A 65 -26.14 -7.21 2.84e+01 1qs1A 462 -37.08 -7.18 2.90e+01 1e8xA 961 -43.03 -7.18 2.91e+01 1jacA 133 -30.00 -7.11 3.04e+01 1im2A 444 -34.05 -7.03 3.19e+01 1f4tA 368 -35.92 -7.03 3.20e+01 1lmzA 187 -33.85 -7.02 3.22e+01 1hg5A 289 -39.33 -7.00 3.27e+01 1dcs 311 -32.56 -6.99 3.28e+01 1jksA 294 -30.47 -6.96 3.34e+01 1bk6A 422 -36.76 -6.96 3.35e+01 1gg3A 279 -31.79 -6.94 3.40e+01 1i2mA 216 -29.26 -6.92 3.44e+01 1chc 68 -27.60 -6.84 3.61e+01 1jbjA 186 -32.04 -6.76 3.82e+01 1pyp 285 -39.68 -6.74 3.85e+01 2kfnA 605 -38.39 -6.72 3.91e+01