PFRMAT SS TARGET T0120 AUTHOR 2000-8506-6614 METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET T0120 METHOD Using neural net overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 9 METHOD 7 10 METHOD 5 9 METHOD 11 3 (1 EHL2 ) METHOD The input amino acid frequencies were determined from METHOD alignment /projects/compbio/tmp/hmm-target99-beta-25498/target-align-25498.a2m METHOD with weighted counts, using EntropyWeight(1.4 bits/column, 10) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 2.01178 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: T0120 METHOD model_file: /projects/compbio/tmp/sam-nn-tmp.beta.2254/model.mod METHOD database_files: /projects/compbio/bin/scripts/hmm-target99-dir/pcc/data/overrep-2260.verify.mixed.seq /projects/compbio/bin/scripts/hmm-target99-dir/pcc/data/overrep-2260.verify.mixed.2d METHOD scoring_mode: local METHOD null_model: reverse METHOD scoring_algorithm: EM METHOD adjust_score: 2 METHOD date: Thu Jul 27 05:38:51 2000 METHOD Method 2: METHOD ###begin 0 METHOD METHOD Protein secondary structure prediction by universal HMM METHOD HMM file: /projects/compbio/bin/scripts/hmm-target99-dir/pcc/scripts/gdac.test.initreest.38state.abb.isites.gd.updated.ghmm-128reest-1-128-105-0.07gd METHOD Alignment file: /projects/compbio/tmp/hmm-target99-beta-25498/target-align-25498.a2m METHOD METHOD guide seq name: T0120 METHOD ###end 0 MODEL 1 M C 0.711 E C 0.559 R C 0.481 K C 0.39 I E 0.362 S E 0.375 R E 0.474 I E 0.518 H E 0.565 L E 0.582 V E 0.492 S C 0.575 E C 0.671 P C 0.673 S C 0.585 I C 0.382 T E 0.383 H E 0.423 F E 0.494 L E 0.533 Q E 0.553 V E 0.567 S E 0.492 W H 0.503 E H 0.523 K H 0.523 T H 0.48 L H 0.478 E H 0.439 S C 0.494 G C 0.667 F E 0.529 V E 0.759 I E 0.784 T E 0.762 L E 0.682 T C 0.534 D C 0.696 G C 0.722 H C 0.632 S C 0.472 A C 0.418 W E 0.475 T E 0.459 G E 0.432 T E 0.513 V E 0.434 S C 0.591 E H 0.51 S H 0.51 E H 0.541 I H 0.505 S H 0.517 Q H 0.61 E H 0.588 A H 0.656 D H 0.653 D H 0.725 M H 0.73 A H 0.695 M H 0.669 E H 0.657 K H 0.613 G C 0.463 K C 0.502 Y H 0.452 V H 0.66 G H 0.72 E H 0.747 L H 0.758 R H 0.767 K H 0.771 A H 0.744 L H 0.724 L H 0.651 S H 0.507 G C 0.663 A C 0.712 G C 0.778 P C 0.7 A C 0.62 D C 0.514 V E 0.478 Y E 0.611 T E 0.654 F E 0.645 N E 0.536 F E 0.453 S C 0.527 K H 0.409 E H 0.434 S H 0.468 C H 0.442 Y H 0.449 F H 0.452 F H 0.462 F H 0.42 E H 0.445 K C 0.414 N C 0.509 L C 0.419 K C 0.409 D C 0.382 V H 0.342 S E 0.385 F E 0.455 R E 0.448 L E 0.374 G C 0.491 S C 0.487 F C 0.467 N C 0.518 L H 0.435 E H 0.423 K H 0.432 V C 0.466 E C 0.576 N C 0.731 P H 0.564 A H 0.673 E H 0.685 V H 0.682 I H 0.687 R H 0.701 E H 0.695 L H 0.659 I H 0.617 C H 0.603 Y H 0.588 C H 0.521 L H 0.53 D H 0.446 T H 0.452 I H 0.52 A H 0.547 E H 0.566 N H 0.518 Q H 0.547 A H 0.544 K H 0.57 N H 0.558 E H 0.609 H H 0.616 L H 0.643 Q H 0.653 K H 0.691 E H 0.678 N H 0.635 E H 0.728 R H 0.705 L H 0.682 L H 0.638 R H 0.55 D H 0.505 W H 0.736 N H 0.692 D H 0.706 V H 0.645 Q H 0.656 G H 0.629 R H 0.611 F H 0.715 E H 0.73 K H 0.718 C H 0.685 V H 0.629 S H 0.603 A H 0.785 K H 0.797 E H 0.811 A H 0.795 L H 0.778 E H 0.773 T H 0.753 D H 0.756 L H 0.757 Y H 0.745 K H 0.693 R H 0.595 F H 0.523 I H 0.5 L H 0.492 V H 0.483 L H 0.481 N H 0.472 E H 0.545 K H 0.6 K H 0.679 T H 0.668 K H 0.711 I H 0.743 R H 0.77 S H 0.776 L H 0.783 H H 0.781 N H 0.819 K H 0.811 L H 0.8 L H 0.794 N H 0.771 A H 0.792 A H 0.783 Q H 0.787 E H 0.78 R H 0.76 E H 0.775 K H 0.775 D H 0.759 I H 0.762 K H 0.751 Q H 0.727 E H 0.516 G C 0.668 E C 0.599 T C 0.411 A E 0.426 I E 0.485 C E 0.413 S C 0.377 E C 0.39 M C 0.425 T C 0.486 A C 0.567 D C 0.676 R C 0.69 D C 0.747 P C 0.696 V C 0.584 Y C 0.548 D C 0.64 E C 0.633 S C 0.679 T C 0.679 D C 0.688 E C 0.518 E C 0.549 S C 0.606 E C 0.616 N C 0.657 Q C 0.515 T C 0.527 D C 0.503 L H 0.484 S C 0.443 G C 0.426 L C 0.404 A H 0.409 S H 0.413 A H 0.395 A H 0.364 V C 0.357 S C 0.518 K C 0.59 D C 0.643 D C 0.589 S C 0.486 I E 0.371 I E 0.363 S C 0.427 S C 0.472 L C 0.537 D C 0.594 V C 0.424 T C 0.455 D C 0.47 I C 0.488 A C 0.599 P C 0.518 S C 0.47 R H 0.615 K H 0.636 R H 0.684 R H 0.717 Q H 0.734 R H 0.731 M H 0.71 Q H 0.682 R H 0.591 N H 0.497 L C 0.515 G C 0.728 T C 0.719 E C 0.669 P C 0.625 K C 0.545 M C 0.531 A C 0.611 P C 0.585 Q C 0.526 E H 0.484 N H 0.463 Q H 0.511 L H 0.53 Q H 0.513 E H 0.477 K C 0.487 E C 0.544 N C 0.652 S C 0.705 R C 0.757 P C 0.752 D C 0.73 S C 0.688 S C 0.683 L C 0.691 P C 0.705 E C 0.6 T C 0.601 S C 0.619 K C 0.471 K H 0.439 E H 0.441 H H 0.38 I C 0.345 S C 0.417 A H 0.478 E H 0.431 N C 0.465 M C 0.515 S C 0.532 L H 0.699 E H 0.697 T H 0.696 L H 0.621 R H 0.531 N C 0.517 S C 0.716 S C 0.788 P H 0.557 E H 0.619 D H 0.623 L H 0.592 F H 0.541 D H 0.514 E H 0.472 I C 0.638 END