% 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.YEL010W.t2k-w0.5.mod Host: cc74 Sat Nov 2 11:10:06 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YEL0/YEL010W % --------------------------------------------------------------------- % Inserted Files: YEL010W.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: YEL010W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 117 nodes, 115.45 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(=3.0244) * Reverse)^tau(=0.7650))) % 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 1btgA 110 -25.05 -7.70 1.09e-01 1sgfY 118 -25.12 -7.65 1.15e-01 1bet 107 -24.92 -7.62 1.19e-01 1ai1H 221 -26.43 -6.46 4.43e-01 1wwwW 120 -23.93 -6.31 5.25e-01 2gatA 66 -22.08 -6.19 6.03e-01 3gatA 66 -22.08 -6.19 6.03e-01 1gatA 60 -21.73 -6.06 7.01e-01 1rec 201 -24.74 -5.82 9.25e-01 1jsa 202 -24.75 -5.82 9.30e-01 1la3A 202 -24.75 -5.73 1.04e+00 2hpaA 342 -26.20 -5.49 1.37e+00 1cviA 342 -26.20 -5.49 1.37e+00 1fpzA 212 -24.72 -5.29 1.75e+00 1bjx 110 -23.03 -5.22 1.91e+00 2bjxA 110 -23.03 -5.22 1.91e+00 2rslA 140 -23.33 -5.18 2.00e+00 1gdtA 183 -23.75 -5.04 2.36e+00 1pcp 106 -22.79 -4.84 3.00e+00 2pspA 106 -22.79 -4.84 3.00e+00 1dpo 223 -23.71 -4.75 3.36e+00 1rpa 342 -25.62 -4.72 3.51e+00 1am1 213 -23.70 -4.66 3.79e+00 1amw 214 -23.70 -4.65 3.81e+00 1bgq 225 -23.75 -4.64 3.88e+00 1ah6 220 -23.73 -4.63 3.92e+00 1a4h 230 -23.77 -4.62 3.98e+00 1egjL 215 -23.91 -4.50 4.58e+00 1fdlH 218 -23.45 -4.43 5.01e+00 1l8pA 436 -25.06 -4.33 5.71e+00 1oneA 436 -25.06 -4.31 5.83e+00 2oneA 436 -25.06 -4.31 5.83e+00 4enl 436 -25.06 -4.30 5.91e+00 1ji0A 240 -23.27 -4.13 7.33e+00 1hcfB 130 -22.23 -3.95 9.31e+00 1gv7A 123 -21.80 -3.70 1.28e+01 1jk9B 249 -22.76 -3.68 1.31e+01 1c4eA 35 -19.08 -3.67 1.33e+01 3trx 105 -22.12 -3.66 1.34e+01 1g1yA 585 -25.11 -3.64 1.39e+01 1jl8A 585 -25.09 -3.62 1.43e+01 1jf6A 585 -25.09 -3.61 1.44e+01 1ji2A 585 -25.09 -3.61 1.44e+01 1bvzA 585 -25.09 -3.61 1.44e+01 1jf5A 585 -25.09 -3.61 1.44e+01 1bolA 222 -23.13 -3.60 1.45e+01 1cs6A 382 -23.59 -3.55 1.57e+01 1erv 105 -22.21 -3.55 1.57e+01 1amm 174 -23.71 -3.52 1.62e+01 4gcr 174 -23.71 -3.52 1.62e+01 1amf 233 -22.41 -3.45 1.80e+01 1wod 233 -22.41 -3.45 1.80e+01 1fgnH 214 -23.97 -3.44 1.80e+01 1hqvA 191 -22.51 -3.37 1.97e+01 1qgvA 142 -21.20 -3.33 2.10e+01 1bihA 395 -23.40 -3.28 2.23e+01 1ldnA 316 -23.20 -3.27 2.27e+01 2ldb 317 -23.20 -3.27 2.28e+01 1d2kA 392 -23.69 -3.26 2.29e+01 1aaf 55 -19.32 -3.25 2.32e+01 1f46A 140 -20.89 -3.19 2.52e+01 1cczA 171 -22.02 -3.18 2.56e+01 1nldH 215 -22.28 -3.17 2.61e+01 1fs1A 53 -19.13 -3.17 2.61e+01 2pcpB 215 -21.95 -3.16 2.62e+01 1f47B 144 -20.92 -3.16 2.64e+01 1k7wA 468 -23.63 -3.13 2.74e+01 1hy1C 468 -23.63 -3.12 2.79e+01 1jv5B 117 -21.44 -3.10 2.85e+01 1quqB 121 -21.16 -3.10 2.87e+01 1bfs 106 -20.72 -3.10 2.88e+01 1uox 296 -22.43 -3.08 2.94e+01 1faxA 255 -22.58 -3.08 2.95e+01 2pkaA 80 -19.96 -3.08 2.95e+01 2kaiA 80 -19.96 -3.08 2.95e+01 1dcnC 434 -23.47 -3.07 2.98e+01 1j5pA 253 -23.16 -3.07 2.99e+01 1dcnD 436 -23.48 -3.05 3.05e+01 1jhlL 108 -21.86 -3.05 3.07e+01 1ert 105 -21.72 -3.05 3.08e+01 1f4pA 147 -22.18 -3.04 3.11e+01 1gpmA 525 -24.08 -3.03 3.13e+01 1ppeI 29 -17.49 -3.03 3.14e+01 1nfiB 107 -20.67 -3.03 3.14e+01 1h2hA 241 -23.08 -3.03 3.15e+01 1aiu 105 -21.63 -3.03 3.16e+01 1hcgA 241 -22.45 -3.02 3.20e+01 1c5mD 255 -22.58 -3.02 3.21e+01 1ghtA 105 -20.44 -3.00 3.26e+01 1ksnA 254 -22.56 -3.00 3.26e+01 1lu0A 29 -17.47 -3.00 3.28e+01 1fmjA 351 -23.83 -2.99 3.32e+01 1pce 60 -19.29 -2.99 3.33e+01 1dcnA 424 -23.36 -2.99 3.34e+01 1qa9B 95 -19.89 -2.96 3.47e+01 1jm4B 118 -20.92 -2.95 3.51e+01 1f68A 103 -21.22 -2.93 3.59e+01 1g2lA 235 -22.30 -2.93 3.61e+01 1iknC 119 -20.84 -2.92 3.64e+01 1kozA 36 -18.41 -2.90 3.74e+01 1poc 134 -21.63 -2.87 3.93e+01