% 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. % --------------------------------------------------------------------- % strfoo.1.YEL014C.t2k-100-30-str Host: cc64 Sat Dec 7 06:59:27 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YEL0/YEL014C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.strs % % 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 YEL014C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL014C.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7458 sequences, 1753770 residues, 102 nodes, 70.25 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(=2.1618) * Reverse)^tau(=0.7359))) % 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 1i7dA 659 -32.10 -10.12 4.55e-01 1d6mA 653 -30.39 -8.66 1.30e+00 1hlcA 129 -27.85 -7.82 2.42e+00 1eur 365 -29.38 -7.28 3.66e+00 1ey2A 471 -31.87 -7.22 3.84e+00 830cA 168 -25.99 -7.10 4.20e+00 1cxvA 164 -25.52 -6.89 4.94e+00 1eybA 471 -31.79 -6.70 5.75e+00 1c8oA 300 -28.34 -6.43 7.12e+00 1dtoA 221 -28.53 -6.30 7.90e+00 1ovaA 386 -28.55 -6.26 8.11e+00 1h6fA 193 -27.60 -6.05 9.64e+00 1qfxA 460 -29.77 -5.95 1.04e+01 1idaA 99 -25.38 -5.59 1.40e+01 1k9vF 201 -25.97 -5.56 1.43e+01 1ha1 184 -24.44 -5.50 1.51e+01 1gpwB 201 -26.03 -5.43 1.59e+01 1d7pM 159 -25.27 -5.42 1.61e+01 1hleA 345 -27.44 -5.38 1.66e+01 4htcI 65 -22.67 -5.37 1.68e+01 1l3kA 196 -24.45 -5.34 1.72e+01 1qlpA 394 -26.87 -5.33 1.73e+01 1k0eA 453 -28.24 -5.25 1.86e+01 9apiA 347 -26.55 -5.20 1.93e+01 1h70A 255 -24.65 -5.07 2.15e+01 1k92A 455 -25.79 -5.05 2.20e+01 1bet 107 -25.07 -5.00 2.29e+01 1d0dA 60 -22.15 -4.99 2.30e+01 1sek 378 -26.86 -4.97 2.35e+01 1dcjA 81 -21.29 -4.91 2.47e+01 1dst 228 -25.71 -4.88 2.54e+01 1lo7A 141 -23.65 -4.86 2.57e+01 1aocA 175 -24.48 -4.86 2.58e+01 1eut 605 -29.99 -4.85 2.61e+01 1jrrA 382 -28.95 -4.76 2.82e+01 1f0cA 305 -27.44 -4.72 2.90e+01 1qhdA 398 -26.92 -4.69 2.99e+01 1ky9B 448 -26.75 -4.68 3.00e+01 1euu 605 -30.00 -4.63 3.13e+01 1dd5A 185 -23.73 -4.60 3.21e+01 1ixmB 192 -23.83 -4.57 3.31e+01 1jevA 517 -26.17 -4.56 3.34e+01 2olbA 517 -26.17 -4.55 3.36e+01 1bxxA 285 -27.48 -4.50 3.50e+01 1l9mA 692 -28.56 -4.47 3.60e+01 2bpa2 175 -26.08 -4.46 3.65e+01 1lci 550 -26.46 -4.43 3.73e+01 1pcfA 66 -21.37 -4.43 3.75e+01 1fhoA 119 -24.67 -4.42 3.78e+01 1h4wA 224 -26.24 -4.42 3.78e+01 1jetA 517 -25.97 -4.38 3.91e+01 1bwyA 132 -24.44 -4.35 3.99e+01