% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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-T2K, 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, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR014W.t2k-100-30-dssp-ehl2 Host: farm17.cse.ucsc.edu Sun Mar 19 21:20:09 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR014W % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR014W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR014W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 1307 nodes, 2391.46 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 (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=1.3389) * Reverse)^tau(=0.7870))) % Calculated when Simple < simple_threshold (10000.00) % 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 1phb 414 -28.84 -15.43 2.16e-01 1yrcA 414 -28.05 -14.88 2.93e-01 1ogoX 574 -51.28 -14.84 2.98e-01 1phg 414 -27.17 -13.94 4.96e-01 1phd 414 -26.86 -13.64 5.89e-01 1dz4A 414 -26.51 -13.38 6.80e-01 5cpp 414 -27.66 -13.30 7.14e-01 1re9A 414 -26.04 -12.90 8.96e-01 1axkA 394 -38.07 -12.86 9.16e-01 2nlrA 234 -35.03 -12.84 9.27e-01 1nlr 234 -35.01 -12.66 1.03e+00 1qmqA 414 -25.57 -12.23 1.32e+00 1wxrA 1048 -53.99 -11.86 1.64e+00 1o20A 427 -25.04 -11.73 1.77e+00 1sqjA 789 -48.25 -11.56 1.96e+00 1gweA 503 -31.48 -10.92 2.84e+00 1gof 639 -59.95 -10.23 4.32e+00 1cknA 330 -32.68 -10.14 4.54e+00 2aamA 309 -24.73 -10.07 4.76e+00 1k32A 1045 -60.48 -10.03 4.86e+00 1pfo 500 -29.67 -9.62 6.26e+00 1m6bA 621 -36.14 -9.61 6.30e+00 1goh 639 -60.78 -9.58 6.40e+00 1x1iA 752 -33.44 -9.54 6.56e+00 1uypA 432 -35.26 -9.42 7.05e+00 1hbzA 498 -29.84 -9.35 7.36e+00 1w2tA 432 -35.60 -9.27 7.74e+00 1xg8A 111 -21.32 -9.14 8.40e+00 1j0mA 752 -33.33 -9.06 8.79e+00 1ijhA 504 -28.65 -8.97 9.32e+00 1m3jA 471 -28.41 -8.94 9.48e+00 1nr0A 611 -56.26 -8.90 9.71e+00 1k3iA 656 -58.28 -8.85 1.00e+01 1ckmA 330 -31.27 -8.69 1.11e+01 1f3eA 386 -21.75 -8.68 1.11e+01 1ju3A 583 -32.94 -8.62 1.16e+01 1pxgA 382 -21.68 -8.57 1.19e+01 2d0oA 610 -24.20 -8.54 1.22e+01 1mxtA 504 -28.23 -8.52 1.24e+01 1n1pA 504 -28.23 -8.52 1.24e+01 1n4wA 504 -28.23 -8.52 1.24e+01 1qbiA 454 -42.71 -8.45 1.28e+01 1dkrA 317 -24.07 -8.42 1.31e+01 1b8sA 504 -28.09 -8.35 1.37e+01 1jfpA 348 -26.43 -8.34 1.38e+01 1b4vA 504 -28.13 -8.30 1.41e+01 1h54B 754 -32.94 -8.28 1.43e+01 1pd21 199 -19.80 -8.27 1.44e+01 2akrA 285 -25.40 -8.25 1.46e+01 1dkuA 317 -22.97 -8.24 1.47e+01 1ibsA 317 -23.69 -8.21 1.50e+01 1srqA 341 -25.61 -8.16 1.54e+01 1xhcA 367 -27.31 -8.15 1.56e+01 1t2bA 397 -21.34 -8.13 1.57e+01 1sy7A 715 -28.15 -8.09 1.62e+01 1sw6A 327 -22.14 -8.08 1.63e+01 1xfdA 723 -43.05 -8.03 1.68e+01 1pnkB 557 -26.50 -7.99 1.72e+01 1gkfB 557 -26.31 -7.98 1.73e+01 1gm7B 557 -26.31 -7.98 1.73e+01 2f6kA 307 -22.69 -7.97 1.74e+01 1s9aA 257 -31.63 -7.96 1.76e+01 1oxdA 227 -27.71 -7.91 1.81e+01 1qwlA 505 -24.38 -7.90 1.83e+01 1h54A 754 -32.01 -7.89 1.83e+01 1gk9B 557 -26.25 -7.88 1.85e+01 1gm9B 557 -26.24 -7.88 1.85e+01 1acc 735 -38.12 -7.85 1.88e+01 1k4gA 386 -20.88 -7.85 1.89e+01 1r5yA 386 -20.67 -7.83 1.91e+01 1gpmA 525 -28.62 -7.80 1.95e+01 1gv9A 260 -30.54 -7.77 1.98e+01 1e3aB 560 -25.69 -7.75 2.01e+01 1ajqB 557 -26.27 -7.71 2.05e+01 1a0qL 212 -30.18 -7.71 2.06e+01 7catA 506 -25.51 -7.69 2.09e+01 1jv2A 957 -59.81 -7.69 2.09e+01 1e4fT 419 -27.90 -7.69 2.09e+01 1c9uA 454 -41.82 -7.67 2.11e+01 1z5lA 285 -25.23 -7.67 2.11e+01 1e15A 499 -23.52 -7.60 2.21e+01 1ddlA 188 -27.01 -7.56 2.27e+01 1msaA 109 -24.58 -7.46 2.41e+01 1clc 639 -26.08 -7.45 2.43e+01 1scs 237 -32.55 -7.42 2.48e+01 1nls 237 -32.68 -7.38 2.54e+01 1jpc 109 -24.52 -7.38 2.55e+01 1ijaA 148 -24.11 -7.37 2.56e+01 1kypA 237 -28.41 -7.32 2.65e+01 2fn0A 437 -22.60 -7.27 2.73e+01 1pud 386 -20.21 -7.26 2.75e+01 1rwhA 757 -32.39 -7.25 2.76e+01 1uacH 114 -21.76 -7.24 2.79e+01 1jb7A 495 -26.71 -7.23 2.80e+01 1a0eA 443 -27.91 -7.22 2.83e+01 3ladA 476 -23.44 -7.14 2.97e+01 1xfxA 777 -35.47 -7.09 3.06e+01 1ehkA 562 -31.85 -7.09 3.07e+01 1aun 208 -23.39 -6.92 3.43e+01 1n6eA 1071 -61.94 -6.91 3.45e+01 1njrA 284 -21.58 -6.90 3.48e+01 1pjpA 226 -30.45 -6.88 3.51e+01 2emo 237 -29.66 -6.86 3.56e+01 1m3iA 471 -26.94 -6.85 3.60e+01 1xhkA 187 -22.13 -6.85 3.60e+01 1itkA 731 -21.56 -6.84 3.62e+01 1i8dA 213 -22.59 -6.82 3.66e+01 1bihA 395 -32.95 -6.81 3.70e+01 1efm 393 -25.18 -6.80 3.70e+01 1umdB 324 -20.24 -6.80 3.72e+01 1qksA 567 -40.59 -6.79 3.74e+01 1dt9A 437 -24.38 -6.77 3.79e+01 1ddzA 496 -22.24 -6.76 3.81e+01 1dqiA 124 -24.07 -6.75 3.84e+01 1jceA 344 -20.74 -6.73 3.88e+01 1jcfA 344 -20.71 -6.72 3.92e+01 1n1bA 549 -29.33 -6.70 3.95e+01