% 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. % --------------------------------------------------------------------- % stridefoo.1.YBL109W.t2k-100-30-stride-ebghtl Host: cc43 Mon Nov 11 11:13:46 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YBL1/YBL109W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds % % 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 YBL109W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YBL109W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 112 nodes, 76.64 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(=1.9728) * Reverse)^tau(=0.7379))) % 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 1jwhC 215 -29.86 -8.78 2.01e+00 1qf8A 182 -28.71 -8.28 2.84e+00 1jxpA 186 -28.59 -8.00 3.46e+00 1i7kA 179 -31.11 -7.74 4.16e+00 1lba 146 -28.30 -7.71 4.23e+00 1ks9A 291 -28.35 -7.59 4.61e+00 1dy9A 187 -27.33 -6.97 7.21e+00 2ucz 165 -32.42 -6.69 8.87e+00 1nfdA 203 -28.87 -6.24 1.24e+01 1a31A 538 -29.57 -6.03 1.46e+01 1qtrA 317 -27.14 -6.01 1.47e+01 1h6uA 308 -29.95 -5.97 1.52e+01 1jbbA 153 -29.88 -5.96 1.54e+01 1jatA 155 -28.95 -5.93 1.57e+01 1i7oA 429 -29.76 -5.73 1.83e+01 1ezvD 245 -26.15 -5.73 1.84e+01 1fo3A 460 -27.05 -5.64 1.97e+01 1a36A 592 -29.20 -5.51 2.17e+01 1jbjA 186 -29.58 -5.45 2.27e+01 1kum 108 -26.23 -5.45 2.28e+01 2e2c 156 -30.27 -5.43 2.31e+01 1qm9A 198 -26.87 -5.31 2.55e+01 1mlcB 218 -27.96 -5.26 2.64e+01 1fsu 492 -29.88 -5.22 2.73e+01 1tcrA 202 -28.55 -5.21 2.74e+01 1liiA 363 -26.05 -5.21 2.74e+01 1jrkA 156 -24.68 -5.21 2.75e+01 1g9mC 185 -26.21 -5.17 2.85e+01 1tubA 440 -27.11 -5.16 2.86e+01 1erzA 303 -25.41 -5.13 2.93e+01 1jatB 138 -28.97 -5.07 3.06e+01 1bt7 186 -26.33 -5.07 3.08e+01 1k30A 368 -25.40 -4.99 3.26e+01 3cd4 182 -26.46 -4.96 3.36e+01 1e5uI 187 -26.05 -4.93 3.44e+01 1g97A 459 -29.35 -4.92 3.46e+01 1qdlB 195 -24.84 -4.87 3.59e+01 1k2eA 156 -24.83 -4.84 3.69e+01 1k26A 156 -24.83 -4.84 3.69e+01 1g9mG 321 -27.77 -4.83 3.73e+01 1be3A 446 -26.10 -4.82 3.74e+01 1l9xA 315 -24.64 -4.81 3.78e+01 1kyoD 248 -24.67 -4.79 3.83e+01 1tlk 154 -25.57 -4.76 3.92e+01 1gkkA 297 -26.04 -4.75 3.97e+01 1h7eA 245 -25.21 -4.75 3.97e+01