PFRMAT SS TARGET T0089 AUTHOR 2000-8506-6614 METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET T0089 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-alpha-18073/target-align-18073.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 61.9588 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: T0089 METHOD model_file: ./tmp.alpha.11463/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: Fri May 19 17:34:52 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-alpha-18073/target-align-18073.a2m METHOD METHOD guide seq name: T0089 METHOD ###end 0 MODEL 1 M C 0.67 I C 0.549 D C 0.512 L C 0.454 S C 0.494 K C 0.511 T C 0.529 V C 0.423 F E 0.572 Y E 0.655 T E 0.674 S E 0.658 I E 0.605 D E 0.474 I C 0.568 G C 0.696 S C 0.591 R C 0.501 Y E 0.461 I E 0.613 K E 0.676 G E 0.716 L E 0.702 V E 0.673 L E 0.591 G E 0.504 K E 0.44 R C 0.442 D C 0.614 Q C 0.665 E E 0.457 W E 0.599 E E 0.653 A E 0.69 L E 0.658 A E 0.558 F E 0.434 S C 0.5 S C 0.448 V C 0.42 K C 0.411 S C 0.426 R C 0.435 G C 0.432 L C 0.438 D C 0.504 E C 0.525 G C 0.541 E C 0.419 I E 0.456 K C 0.399 D C 0.555 A H 0.713 I H 0.735 A H 0.739 F H 0.724 K H 0.765 E H 0.764 S H 0.76 V H 0.777 N H 0.772 T H 0.784 L H 0.77 L H 0.786 K H 0.79 E H 0.792 L H 0.789 E H 0.76 E H 0.745 Q H 0.7 L H 0.621 Q C 0.599 K C 0.617 S C 0.493 L C 0.472 R C 0.567 S C 0.572 D C 0.392 F E 0.556 V E 0.596 I E 0.597 S E 0.512 F E 0.403 S C 0.507 S C 0.488 V C 0.472 S E 0.429 F E 0.488 E E 0.515 R E 0.492 E E 0.399 D C 0.493 T C 0.452 V E 0.486 I E 0.547 E E 0.588 R E 0.613 D E 0.572 F E 0.477 G C 0.546 E C 0.655 E C 0.637 K C 0.595 R C 0.522 S C 0.411 I C 0.424 T C 0.654 L H 0.725 D H 0.787 I H 0.786 L H 0.803 S H 0.81 E H 0.82 M H 0.812 Q H 0.81 S H 0.814 E H 0.811 A H 0.782 L H 0.754 E H 0.697 K H 0.639 L H 0.516 K C 0.471 E C 0.484 N C 0.512 G C 0.538 K C 0.47 T E 0.437 P E 0.546 L E 0.547 H E 0.481 I E 0.426 F C 0.486 S C 0.527 K C 0.424 R E 0.416 Y E 0.515 L E 0.515 L E 0.394 D C 0.584 D C 0.609 E C 0.556 R C 0.501 I C 0.534 V C 0.537 F C 0.552 N C 0.706 P C 0.552 L C 0.481 D C 0.501 M C 0.491 K C 0.45 A C 0.462 S C 0.448 K C 0.38 I E 0.408 A E 0.481 I E 0.515 E E 0.531 Y E 0.605 T E 0.641 S E 0.669 I E 0.655 V E 0.559 V C 0.439 P C 0.544 L H 0.456 K H 0.537 V H 0.619 Y H 0.675 E H 0.735 M H 0.742 F H 0.771 Y H 0.773 N H 0.767 F H 0.766 L H 0.757 Q H 0.762 D H 0.752 T H 0.631 V C 0.607 K C 0.656 S C 0.479 P E 0.456 F E 0.494 Q E 0.557 L E 0.597 K E 0.572 S E 0.427 S C 0.45 L H 0.479 V H 0.614 S H 0.666 T H 0.669 A H 0.664 E H 0.652 G H 0.617 V H 0.511 L C 0.498 T C 0.588 T C 0.592 P C 0.506 E C 0.482 K C 0.504 D C 0.57 R C 0.558 G C 0.573 V E 0.581 V E 0.706 V E 0.732 V E 0.695 N E 0.556 L C 0.543 G C 0.754 Y C 0.774 N C 0.739 F C 0.544 T E 0.466 G E 0.585 L E 0.685 I E 0.693 A E 0.692 Y E 0.632 K E 0.457 N C 0.58 G C 0.609 V E 0.489 P E 0.61 I E 0.628 K E 0.55 I C 0.452 S C 0.532 Y C 0.427 V E 0.414 P C 0.457 V C 0.5 G C 0.639 M H 0.48 K H 0.52 H H 0.553 V H 0.574 I H 0.611 K H 0.725 D H 0.726 V H 0.751 S H 0.76 A H 0.755 V H 0.738 L H 0.701 D H 0.602 T H 0.472 S C 0.46 F H 0.638 E H 0.626 E H 0.682 S H 0.761 E H 0.762 R H 0.75 L H 0.711 I H 0.696 I H 0.656 T H 0.628 H H 0.572 G H 0.481 N H 0.445 A C 0.432 V C 0.452 Y C 0.503 N C 0.538 D C 0.54 L C 0.558 K C 0.567 E C 0.535 E C 0.386 E E 0.47 I E 0.498 Q E 0.453 Y E 0.388 R C 0.408 G C 0.402 L C 0.441 D C 0.536 G C 0.586 N C 0.608 T C 0.589 I C 0.562 K C 0.453 T C 0.392 T C 0.442 T C 0.61 A H 0.809 K H 0.856 K H 0.859 L H 0.861 S H 0.872 V H 0.883 I H 0.868 I H 0.854 H H 0.867 A H 0.861 R H 0.855 L H 0.857 R H 0.88 E H 0.864 I H 0.853 M H 0.851 S H 0.854 K H 0.86 S H 0.869 K H 0.881 K H 0.875 F H 0.863 F H 0.856 R H 0.821 E H 0.807 V H 0.671 E C 0.586 A C 0.634 K C 0.628 I C 0.511 V C 0.457 E H 0.439 E H 0.439 G C 0.429 E H 0.45 I C 0.42 G C 0.426 I C 0.538 P C 0.579 G C 0.567 G E 0.48 V E 0.725 V E 0.789 L E 0.761 T E 0.572 G C 0.636 G C 0.652 G C 0.512 A C 0.442 K C 0.441 I C 0.441 P H 0.546 R H 0.618 I H 0.744 N H 0.778 E H 0.794 L H 0.784 A H 0.783 T H 0.774 E H 0.752 V H 0.719 F H 0.59 K C 0.569 S C 0.611 P C 0.514 V E 0.447 R E 0.526 T E 0.513 G C 0.431 C C 0.531 Y C 0.594 A C 0.585 N C 0.622 S C 0.691 D C 0.646 R C 0.627 P C 0.579 S C 0.524 I C 0.457 I C 0.472 N C 0.605 A C 0.57 D C 0.435 E H 0.43 V H 0.423 A C 0.393 N C 0.58 D C 0.773 P H 0.474 S H 0.575 F H 0.597 A H 0.588 A H 0.583 A H 0.599 F H 0.595 G H 0.57 N H 0.552 V H 0.566 F H 0.559 A H 0.542 V H 0.474 S H 0.402 E C 0.379 N C 0.468 P C 0.559 Y C 0.559 E C 0.545 E C 0.496 T C 0.503 P C 0.529 V C 0.566 K C 0.61 S C 0.615 E C 0.548 N C 0.496 P H 0.492 L H 0.598 K H 0.62 K H 0.629 I H 0.647 F H 0.629 R H 0.648 L H 0.594 F H 0.533 K H 0.549 E H 0.482 L C 0.453 M C 0.526 E C 0.603 END