% 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. % --------------------------------------------------------------------- % w0.5foo.1.YGR027W-A.t2k-w0.5.mod Host: cc51 Fri Nov 8 18:48:31 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR027W-A % --------------------------------------------------------------------- % Inserted Files: YGR027W-A.t2k-w0.5.mod % Database Files: /projects/compbio/experiments/protein-predict/SAM_T02/data/pdbaa % % 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)) % Single Track Model: YGR027W-A.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 441 nodes, 452.04 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(=2.7803) * Reverse)^tau(=0.6771))) % 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 1fonA 240 -28.56 -7.13 3.83e+00 1gtmA 419 -29.95 -7.10 3.90e+00 1gjyA 167 -27.32 -7.01 4.16e+00 1qkkA 155 -26.82 -6.63 5.49e+00 2gsaA 432 -28.79 -6.15 7.83e+00 1a6i 217 -27.27 -5.93 9.25e+00 2trt 217 -27.27 -5.91 9.44e+00 1a4eA 488 -28.31 -5.79 1.03e+01 1pvaA 110 -24.77 -5.68 1.13e+01 1f4qA 165 -25.73 -5.52 1.27e+01 1fntC 245 -28.08 -5.45 1.34e+01 1rypC 244 -28.08 -5.45 1.34e+01 1ltm 320 -27.36 -5.27 1.54e+01 1qusA 322 -27.36 -5.27 1.55e+01 1bsg 266 -26.14 -5.22 1.61e+01 1k94A 165 -25.35 -5.14 1.71e+01 1ydrE 350 -27.70 -5.09 1.78e+01 1bvuA 418 -29.27 -5.09 1.79e+01 1kynB 235 -25.74 -5.08 1.80e+01 1stcE 350 -27.60 -5.05 1.84e+01 1l7oA 211 -26.61 -4.90 2.08e+01 1l7mA 211 -26.61 -4.89 2.09e+01 1iow 306 -25.97 -4.77 2.31e+01 1j97A 211 -26.42 -4.74 2.36e+01 1f5sA 211 -26.42 -4.73 2.38e+01 1bx6 350 -27.61 -4.69 2.46e+01 1xyzA 347 -27.02 -4.69 2.46e+01 1rcoB 475 -27.59 -4.69 2.47e+01 1fmoE 350 -27.61 -4.67 2.50e+01 8rucA 475 -27.58 -4.67 2.51e+01 1rxoB 475 -27.58 -4.67 2.52e+01 1fftC 204 -24.97 -4.59 2.66e+01 1l3rE 350 -27.61 -4.57 2.72e+01 1jbpE 350 -27.67 -4.55 2.76e+01 2dln 306 -25.78 -4.55 2.76e+01 1mroA 548 -27.75 -4.52 2.83e+01 1hbnA 549 -27.76 -4.52 2.83e+01 1cmkE 350 -27.30 -4.48 2.93e+01 1cdkA 350 -27.30 -4.48 2.93e+01 1cghA 224 -25.03 -4.48 2.94e+01 1au8A 224 -25.03 -4.48 2.94e+01 1h67A 108 -25.09 -4.45 2.99e+01 1bjz 207 -25.70 -4.43 3.05e+01 2tct 207 -25.70 -4.43 3.06e+01 1ctpE 350 -27.21 -4.42 3.08e+01 1fpn1 289 -26.87 -4.39 3.16e+01 1xys 347 -27.32 -4.37 3.22e+01 1e5nA 348 -27.32 -4.37 3.22e+01 1ii6A 368 -27.00 -4.32 3.34e+01 1kyqA 274 -25.81 -4.24 3.59e+01 1hmjA 78 -22.99 -4.20 3.70e+01 1ck4B 198 -25.32 -4.20 3.71e+01 1atpE 350 -27.22 -4.15 3.86e+01 1qpiA 203 -25.37 -4.14 3.90e+01 1apmE 350 -27.21 -4.13 3.92e+01 1clxA 347 -27.09 -4.12 3.95e+01