PFRMAT SS TARGET T0116 AUTHOR 2000-8506-6614 METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET T0116 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-30545/target-align-30545.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 101.719 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: T0116 METHOD model_file: /projects/compbio/tmp/sam-nn-tmp.beta.26425/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: Tue Jul 25 06:16:51 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-30545/target-align-30545.a2m METHOD METHOD guide seq name: T0116 METHOD ###end 0 MODEL 1 M C 0.642 E C 0.563 G C 0.565 M C 0.577 L C 0.635 K C 0.692 G C 0.534 E C 0.509 G C 0.525 P C 0.46 G C 0.476 P C 0.484 L C 0.556 P C 0.623 P H 0.581 L H 0.616 L H 0.683 Q H 0.699 Q H 0.688 Y H 0.678 V H 0.655 E H 0.635 L H 0.601 R H 0.578 D H 0.517 Q C 0.473 Y C 0.631 P C 0.603 D C 0.538 Y E 0.558 L E 0.625 L E 0.637 L E 0.629 F E 0.594 Q E 0.505 V C 0.468 G C 0.592 D C 0.484 F E 0.391 Y E 0.46 E E 0.453 C H 0.387 F H 0.402 G H 0.463 E H 0.553 D H 0.636 A H 0.688 E H 0.689 R H 0.684 L H 0.679 A H 0.68 R H 0.683 A H 0.671 L H 0.627 G H 0.541 L H 0.5 V H 0.449 L E 0.374 T E 0.402 H E 0.4 K C 0.413 T C 0.53 S C 0.621 K C 0.662 D C 0.623 F C 0.606 T C 0.576 T C 0.464 P C 0.435 M E 0.402 A C 0.414 G C 0.486 I C 0.584 P C 0.65 L H 0.552 R H 0.588 A H 0.602 F H 0.658 E H 0.682 A H 0.704 Y H 0.703 A H 0.73 E H 0.746 R H 0.74 L H 0.729 L H 0.707 K H 0.683 M H 0.588 G C 0.644 F C 0.601 R E 0.51 L E 0.632 A E 0.625 V E 0.617 A E 0.554 D E 0.438 Q C 0.444 V C 0.511 E C 0.582 P C 0.655 A H 0.522 E H 0.552 E H 0.591 A H 0.515 E C 0.459 G C 0.59 L C 0.501 V C 0.399 R H 0.422 R H 0.421 E H 0.382 V E 0.46 T E 0.452 Q E 0.444 L E 0.428 L C 0.427 T C 0.673 P C 0.694 G C 0.682 T C 0.6 L C 0.513 L C 0.522 Q C 0.539 E C 0.465 S C 0.452 L C 0.444 L C 0.486 P C 0.581 R C 0.567 E C 0.587 A C 0.574 N C 0.569 Y E 0.374 L E 0.526 A E 0.577 A E 0.592 I E 0.582 A E 0.527 T C 0.482 G C 0.613 D C 0.565 G E 0.462 W E 0.555 G E 0.578 L E 0.61 A E 0.621 F E 0.623 L E 0.586 D E 0.48 V C 0.477 S C 0.556 T C 0.568 G C 0.528 E E 0.46 F E 0.555 K E 0.573 G E 0.547 T E 0.427 V C 0.43 L C 0.507 K C 0.598 S C 0.645 K H 0.51 S H 0.63 A H 0.671 L H 0.693 Y H 0.701 D H 0.708 E H 0.701 L H 0.689 F H 0.648 R H 0.582 H C 0.479 R C 0.683 P C 0.562 A C 0.421 E E 0.448 V E 0.57 L E 0.569 L E 0.448 A C 0.558 P C 0.598 E C 0.581 L C 0.547 L C 0.535 E C 0.459 N C 0.453 G H 0.492 A H 0.538 F H 0.563 L H 0.581 D H 0.57 E H 0.58 F H 0.578 R H 0.561 K H 0.546 R H 0.476 F H 0.458 P H 0.423 V C 0.402 M C 0.424 L C 0.444 S C 0.488 E C 0.425 A C 0.417 P H 0.42 F C 0.433 E H 0.449 P H 0.467 E H 0.476 G H 0.448 E H 0.443 G C 0.476 P H 0.442 L H 0.583 A H 0.655 L H 0.669 R H 0.685 R H 0.698 A H 0.707 R H 0.714 G H 0.699 A H 0.698 L H 0.7 L H 0.706 A H 0.699 Y H 0.689 A H 0.68 Q H 0.662 R H 0.648 T H 0.544 Q H 0.448 G H 0.473 G C 0.443 A C 0.441 L C 0.465 S C 0.5 L C 0.452 Q C 0.458 P C 0.458 F C 0.436 R C 0.366 F E 0.38 Y E 0.374 D C 0.411 P C 0.438 G C 0.493 A C 0.446 F E 0.356 M E 0.45 R E 0.482 L E 0.431 P C 0.511 E H 0.628 A H 0.653 T H 0.664 L H 0.68 R H 0.667 A H 0.658 L H 0.639 E H 0.571 V H 0.539 F H 0.395 E C 0.446 P C 0.532 L C 0.564 R C 0.636 G C 0.669 Q C 0.646 D C 0.496 T C 0.383 L H 0.609 F H 0.616 S H 0.629 V H 0.604 L H 0.583 D H 0.464 E H 0.466 T C 0.419 R C 0.417 T C 0.467 A H 0.524 P H 0.564 G H 0.595 R H 0.642 R H 0.657 L H 0.663 L H 0.665 Q H 0.649 S H 0.629 W H 0.57 L H 0.507 R C 0.421 H C 0.669 P C 0.665 L C 0.601 L C 0.614 D C 0.65 R H 0.667 G H 0.684 P H 0.707 L H 0.739 E H 0.742 A H 0.75 R H 0.756 L H 0.771 D H 0.763 R H 0.774 V H 0.793 E H 0.799 G H 0.788 F H 0.771 V H 0.747 R H 0.699 E H 0.664 G H 0.687 A H 0.698 L H 0.711 R H 0.732 E H 0.74 G H 0.737 V H 0.741 R H 0.741 R H 0.737 L H 0.709 L H 0.689 Y H 0.608 R H 0.562 L C 0.466 A C 0.497 D H 0.469 L H 0.774 E H 0.777 R H 0.79 L H 0.775 A H 0.768 T H 0.753 R H 0.747 L H 0.72 E H 0.666 L H 0.6 G C 0.491 R C 0.516 A C 0.546 S C 0.588 P H 0.661 K H 0.695 D H 0.701 L H 0.729 G H 0.724 A H 0.721 L H 0.727 R H 0.73 R H 0.72 S H 0.708 L H 0.715 Q H 0.697 I H 0.687 L H 0.702 P H 0.723 E H 0.73 L H 0.74 R H 0.751 A H 0.747 L H 0.737 L H 0.716 G H 0.647 E H 0.568 E H 0.468 V C 0.443 G C 0.473 L C 0.502 P C 0.503 D C 0.491 L H 0.634 S H 0.661 P H 0.695 L H 0.735 K H 0.754 E H 0.756 E H 0.748 L H 0.739 E H 0.717 A H 0.7 A H 0.666 L H 0.62 V H 0.576 E H 0.511 D C 0.44 P H 0.517 P H 0.537 L H 0.52 K H 0.462 V H 0.402 S C 0.532 E C 0.553 G C 0.517 G C 0.419 L E 0.435 I E 0.42 R C 0.452 E C 0.547 G C 0.605 Y C 0.59 D C 0.594 P H 0.643 D H 0.655 L H 0.762 D H 0.776 A H 0.791 L H 0.79 R H 0.8 A H 0.798 A H 0.793 H H 0.798 R H 0.802 E H 0.799 G H 0.791 V H 0.807 A H 0.82 Y H 0.815 F H 0.815 L H 0.819 E H 0.822 L H 0.816 E H 0.811 E H 0.811 R H 0.8 E H 0.768 R H 0.743 E H 0.712 R H 0.669 T H 0.517 G C 0.623 I C 0.626 P C 0.579 T C 0.451 L E 0.423 K E 0.5 V E 0.54 G E 0.525 Y E 0.497 N E 0.425 A C 0.442 V C 0.477 F C 0.453 G C 0.448 Y E 0.552 Y E 0.614 L E 0.619 E E 0.595 V E 0.531 T C 0.461 R C 0.492 P C 0.469 Y H 0.473 Y H 0.452 E H 0.418 R C 0.435 V C 0.56 P C 0.586 K C 0.522 E C 0.409 Y E 0.47 R E 0.505 P E 0.492 V E 0.459 Q E 0.387 T C 0.407 L C 0.45 K C 0.537 D C 0.532 R C 0.393 Q E 0.432 R E 0.499 Y E 0.464 T C 0.485 L C 0.511 P H 0.663 E H 0.689 M H 0.73 K H 0.742 E H 0.745 K H 0.745 E H 0.746 R H 0.768 E H 0.772 V H 0.775 Y H 0.762 R H 0.765 L H 0.769 E H 0.77 A H 0.774 L H 0.772 I H 0.772 R H 0.766 R H 0.773 R H 0.765 E H 0.771 E H 0.793 E H 0.799 V H 0.792 F H 0.796 L H 0.806 E H 0.798 V H 0.792 R H 0.784 E H 0.784 R H 0.773 A H 0.758 K H 0.743 R H 0.733 Q H 0.722 A H 0.718 E H 0.73 A H 0.739 L H 0.749 R H 0.744 E H 0.745 A H 0.738 A H 0.742 R H 0.739 I H 0.731 L H 0.725 A H 0.705 E H 0.699 L H 0.693 D H 0.672 V H 0.71 Y H 0.713 A H 0.712 A H 0.703 L H 0.714 A H 0.701 E H 0.685 V H 0.678 A H 0.659 V H 0.627 R H 0.593 Y C 0.471 G C 0.656 Y C 0.595 V C 0.53 R C 0.559 P C 0.513 R C 0.455 F C 0.438 G C 0.601 D C 0.584 R C 0.38 L E 0.524 Q E 0.549 I E 0.518 R E 0.38 A C 0.511 G C 0.642 R C 0.679 H C 0.69 P C 0.532 V E 0.394 V E 0.42 E E 0.388 R C 0.404 R C 0.538 T C 0.597 E C 0.588 F C 0.477 V C 0.52 P C 0.619 N C 0.619 D C 0.523 L E 0.444 E E 0.489 M E 0.432 A C 0.558 H C 0.637 E C 0.45 L E 0.654 V E 0.739 L E 0.777 I E 0.742 T E 0.597 G C 0.639 P C 0.741 N C 0.734 M C 0.671 A C 0.712 G C 0.66 K H 0.449 S H 0.576 T H 0.628 F H 0.643 L H 0.676 R H 0.698 Q H 0.712 T H 0.711 A H 0.698 L H 0.693 I H 0.694 A H 0.69 L H 0.689 L H 0.691 A H 0.681 Q H 0.654 V H 0.579 G C 0.516 S C 0.56 F C 0.527 V C 0.574 P C 0.624 A C 0.469 E C 0.439 E H 0.428 A C 0.454 H C 0.433 L C 0.378 P C 0.487 L H 0.516 F H 0.571 D H 0.577 G H 0.503 I E 0.427 Y E 0.454 T E 0.383 R E 0.385 I C 0.408 G C 0.615 A C 0.528 S C 0.498 D H 0.51 D H 0.512 L H 0.547 A H 0.521 G H 0.489 G C 0.489 K C 0.44 S H 0.505 T H 0.614 F H 0.633 M H 0.647 V H 0.687 E H 0.703 M H 0.724 E H 0.736 E H 0.743 V H 0.739 A H 0.736 L H 0.728 I H 0.716 L H 0.702 K H 0.64 E H 0.571 A C 0.522 T C 0.597 E C 0.528 N C 0.544 S C 0.393 L E 0.471 V E 0.598 L E 0.593 L E 0.489 D H 0.368 E H 0.427 V C 0.424 G C 0.578 R C 0.641 G C 0.649 T C 0.635 S C 0.635 S H 0.476 L H 0.544 D H 0.581 G H 0.631 V H 0.67 A H 0.693 I H 0.706 A H 0.711 T H 0.726 A H 0.731 V H 0.733 A H 0.746 E H 0.748 A H 0.733 L H 0.699 H H 0.683 E H 0.657 R H 0.554 R C 0.549 A C 0.521 Y C 0.347 T E 0.545 L E 0.579 F E 0.563 A E 0.465 T H 0.356 H C 0.394 Y H 0.575 F H 0.617 E H 0.62 L H 0.621 T H 0.61 A H 0.61 L H 0.568 G C 0.425 L C 0.514 P C 0.518 R C 0.493 L C 0.388 K E 0.404 N E 0.48 L E 0.511 H E 0.519 V E 0.534 A E 0.529 A E 0.541 R E 0.528 E E 0.467 E C 0.47 A C 0.604 G C 0.619 G C 0.496 L E 0.49 V E 0.565 F E 0.586 Y E 0.586 H E 0.58 Q E 0.575 V E 0.548 L E 0.419 P C 0.476 G C 0.608 P C 0.598 A C 0.609 S C 0.552 K C 0.458 S H 0.529 Y H 0.573 G H 0.569 V H 0.569 E H 0.583 V H 0.657 A H 0.682 A H 0.686 M H 0.675 A H 0.605 G C 0.629 L C 0.706 P C 0.685 K H 0.685 E H 0.704 V H 0.711 V H 0.738 A H 0.754 R H 0.767 A H 0.78 R H 0.778 A H 0.774 L H 0.757 L H 0.742 Q H 0.727 A H 0.732 M H 0.705 A H 0.708 A H 0.708 R H 0.694 R H 0.688 E H 0.697 G H 0.704 A H 0.683 L H 0.703 D H 0.708 A H 0.715 V H 0.73 L H 0.752 E H 0.771 R H 0.765 L H 0.76 L H 0.749 A H 0.729 L H 0.666 D H 0.573 P H 0.545 D H 0.478 R H 0.478 L C 0.455 T C 0.499 P H 0.701 L H 0.753 E H 0.766 A H 0.778 L H 0.786 R H 0.783 L H 0.773 L H 0.771 Q H 0.775 E H 0.753 L H 0.721 K H 0.65 A H 0.546 L C 0.628 A H 0.934 L H 0.916 G H 0.884 A H 0.596 P H 0.506 L H 0.732 D H 0.683 T H 0.566 M C 0.549 K C 0.760 G C 0.979 END