PFRMAT SS TARGET seed-seqs-29121.a2m(1), 200 bases, F33836C checksum. AUTHOR UCSC Target99 server METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET seed-seqs-29121.a2m(1) 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 /var/tmp/hmm-target99-work-25725//target-align-25725.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 82.1097 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: seed-seqs-29121.a2m(1) METHOD model_file: /projects/compbio/tmp/sam-nn-tmp.cc57.3230/model.mod METHOD database_files: /projects/compbio/programs/hmm-server-2.0/src/pcc/data/overrep-2260.verify.mixed.seq /projects/compbio/programs/hmm-server-2.0/src/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: Mon Feb 16 09:31:25 2004 METHOD Method 2: METHOD ###begin 0 METHOD METHOD Protein secondary structure prediction by universal HMM METHOD HMM file: /projects/compbio/programs/hmm-server-2.0/src/pcc/scripts/gdac.test.initreest.38state.abb.isites.gd.updated.ghmm-128reest-1-128-105-0.07gd METHOD Alignment file: /var/tmp/hmm-target99-work-25725//target-align-25725.a2m METHOD METHOD guide seq name: seed-seqs-29121.a2m(1), 200 bases, F33836C checksum. METHOD ###end 0 MODEL 1 M C 0.692 L C 0.571 K C 0.537 N C 0.617 T C 0.555 S C 0.587 S C 0.57 N C 0.622 L C 0.612 D C 0.565 A C 0.526 P C 0.505 V C 0.458 A C 0.473 R H 0.467 S H 0.469 C H 0.487 D H 0.488 F H 0.443 A C 0.483 M C 0.479 K C 0.504 K C 0.53 M H 0.578 D H 0.607 L H 0.639 R H 0.622 K H 0.611 A H 0.597 F H 0.554 T H 0.491 L H 0.367 I C 0.401 E C 0.595 P C 0.672 G C 0.677 P C 0.559 V E 0.623 T E 0.717 L E 0.762 V E 0.737 T E 0.628 T E 0.442 S C 0.629 A C 0.676 G C 0.684 G C 0.641 T C 0.499 N E 0.414 N E 0.409 V E 0.432 M E 0.424 T E 0.408 I E 0.405 S E 0.369 W E 0.404 T E 0.428 M E 0.427 A E 0.449 V E 0.425 D C 0.454 F C 0.599 T C 0.743 P C 0.787 K C 0.687 L E 0.587 A E 0.665 I E 0.676 T E 0.63 T E 0.523 G C 0.566 P C 0.621 W C 0.568 N H 0.438 F H 0.485 S H 0.561 Y H 0.637 K H 0.642 A H 0.638 L H 0.641 T H 0.632 K H 0.627 S H 0.473 R C 0.598 E C 0.394 C E 0.602 V E 0.637 I E 0.616 A E 0.503 I C 0.417 P C 0.552 T C 0.577 V H 0.615 D H 0.62 L H 0.654 L H 0.663 D H 0.665 K H 0.659 V H 0.643 V H 0.625 G H 0.601 V H 0.541 G H 0.45 T C 0.438 C C 0.504 S C 0.621 G C 0.685 K C 0.646 D C 0.635 T C 0.515 D C 0.535 K H 0.551 F H 0.559 D H 0.56 T H 0.541 F H 0.441 R C 0.61 L C 0.545 T C 0.448 P C 0.448 I C 0.468 K C 0.498 G C 0.54 K C 0.502 Y C 0.482 V C 0.511 E C 0.668 A C 0.626 P C 0.536 L H 0.465 I H 0.525 K H 0.558 E H 0.534 C C 0.517 V C 0.395 A E 0.493 N E 0.534 I E 0.555 E E 0.541 C E 0.533 K E 0.538 V E 0.535 V E 0.497 D E 0.473 I E 0.439 I E 0.39 K C 0.477 K C 0.599 H C 0.536 D E 0.46 I E 0.614 V E 0.647 V E 0.631 L E 0.588 E E 0.584 G E 0.611 V E 0.583 A E 0.547 A E 0.523 Y E 0.483 F E 0.403 D C 0.472 T C 0.49 S C 0.466 R C 0.422 K C 0.485 E C 0.666 K C 0.656 R C 0.61 T C 0.522 L E 0.419 H E 0.501 A E 0.504 V E 0.396 G C 0.536 D C 0.591 G C 0.56 T C 0.408 F E 0.539 V E 0.546 V E 0.476 D C 0.451 G C 0.588 R C 0.528 T C 0.443 L H 0.417 D H 0.415 R H 0.474 K H 0.459 K H 0.458 Q H 0.469 M H 0.435 R H 0.412 S C 0.431 K C 0.402 L C 0.421 L C 0.479 G C 0.553 I C 0.748 F C 0.733 END