=========================================================================
This is a sample history file of commands which were used to train the
GeneZilla gene finder on a set of ~8000 human training genes. As can be
seen from the time stamps, the entire process took approximately 5 hours
(split over two days) and nearly 500 commands. A novice can expect the
process to take somewhat longer, due to unfamiliarity with the software
and training process. Note, furthermore, that the following constitutes
only a basic training session without further optimization steps to fine-
tune the gene finder. The auto-trainer GRAPE was not used. Also note
that edits to the *.iso and *.cfg files are not shown. See the training
manual for additional information. Futher updates to the software may
necessitate changes to the following commands as additional parameters are
introduced. (contact: bmajoros@tigr.org)
=========================================================================
443 13:56 cd refseq
446 13:56 mkdir train
447 13:56 cd train
449 13:56 ln -s ../train.gff iso0-100.gff
450 13:56 ln -s ../train.fasta iso0-100.fasta
452 13:57 ln -s /home/bmajoros/GF/genezilla
459 14:00 genezilla/split-by-isochore.pl iso0-100.gff iso0-100.fasta . 4 0 43 51 57 100
462 14:09 mkdir iso0-43
463 14:09 mkdir iso43-51
464 14:09 mkdir iso51-57
465 14:09 mkdir iso57-100
466 14:09 mv iso0-43.* iso0-43
467 14:09 mv iso43-51.* iso43-51
468 14:10 mv iso51-57.* iso51-57
469 14:10 mv iso57-100.* iso57-100
471 14:10 cd iso0-43
473 14:10 ln -s ~/GF/genezilla
475 14:11 genezilla/get-examples.pl iso0-43.gff iso0-43.fasta TAG,TGA,TAA notrim
478 14:21 genezilla/get-negative-examples.pl .
480 14:21 cd ../iso43-51
482 14:22 genezilla/get-examples.pl iso43-51.gff iso43-51.fasta TAG,TGA,TAA notrim
483 14:22 ln -s ~/GF/genezilla
484 14:22 genezilla/get-examples.pl iso43-51.gff iso43-51.fasta TAG,TGA,TAA notrim
485 14:24 genezilla/get-negative-examples.pl .
486 14:24 cd ../iso51-57
487 14:25 ln -s ~/GF/genezilla
488 14:25 genezilla/get-examples.pl iso51-57.gff iso51-57.fasta TAG,TGA,TAA notrim
489 14:26 genezilla/get-negative-examples.pl .
490 14:26 cd ../iso57-100
491 14:26 ln -s ~/GF/genezilla
492 14:26 genezilla/get-examples.pl iso57-100.gff iso57-100.fasta TAG,TGA,TAA notrim
493 14:33 genezilla/get-negative-examples.pl .
495 14:42 cd ../iso0-43
508 14:58 genezilla/get-duration-distr.pl initial-exons0-43.fasta 50 20 0 0 > initial-exons0-43.distr.baseline
520 15:11 genezilla/get-duration-distr.pl initial-exons0-43.fasta 50 4 1 0 0 > initial-exons0-43.distr ; xgraph initial-exons0-43.distr initial-exons0-43.distr.baseline
522 15:13 genezilla/get-duration-distr.pl internal-exons0-43.fasta 50 2 0 0 0 > internal-exons0-43.distr.baseline
521 15:13 genezilla/get-duration-distr.pl internal-exons0-43.fasta 50 4 1 0 0 > internal-exons0-43.distr ; xgraph internal-exons0-43.distr internal-exons0-43.distr.baseline
523 15:14 genezilla/get-duration-distr.pl final-exons0-43.fasta 50 4 0 0 0 > final-exons0-43.distr.baseline
526 15:15 genezilla/get-duration-distr.pl final-exons0-43.fasta 50 4 4 0 0 > final-exons0-43.distr ; xgraph final-exons0-43.distr final-exons0-43.distr.baseline
527 15:17 genezilla/get-duration-distr.pl single-exons0-43.fasta 50 4 0 0 0 > single-exons0-43.distr.baseline
569 16:11 genezilla/get-duration-distr.pl single-exons0-43.fasta 25 2 12 4 1.05 > single-exons0-43.distr ; xgraph -lw 2 single-exons0-43.distr single-exons0-43.distr.baseline
572 16:16 cd ../iso43-51
577 16:17 genezilla/get-duration-distr.pl single-exons43-51.fasta 25 0 0 0 0 > single-exons43-51.distr.baseline
579 16:19 genezilla/get-duration-distr.pl single-exons43-51.fasta 25 2 12 4 1.02 > single-exons43-51.distr ; xgraph -lw 2 single-exons43-51.distr single-exons43-51.distr.baseline
581 16:23 genezilla/get-duration-distr.pl initial-exons43-51.fasta 50 0 0 0 0 > initial-exons43-51.distr.baseline
580 16:22 genezilla/get-duration-distr.pl initial-exons43-51.fasta 50 4 1 0 0 > initial-exons43-51.distr ; xgraph initial-exons43-51.distr initial-exons43-51.distr.baseline
583 16:24 genezilla/get-duration-distr.pl internal-exons43-51.fasta 50 0 0 0 0 > internal-exons43-51.distr.baseline
582 16:23 genezilla/get-duration-distr.pl internal-exons43-51.fasta 50 4 1 0 0 > internal-exons43-51.distr ; xgraph internal-exons43-51.distr internal-exons43-51.distr.baseline
585 16:25 genezilla/get-duration-distr.pl final-exons43-51.fasta 50 0 0 0 0 > final-exons43-51.distr.baseline
598 16:30 genezilla/get-duration-distr.pl final-exons43-51.fasta 25 4 4 3 1.01 > final-exons43-51.distr ; xgraph -lw 2 final-exons43-51.distr final-exons43-51.distr.baseline
601 16:31 cd ../iso51-57
604 16:32 genezilla/get-duration-distr.pl single-exons51-57.fasta 25 0 0 0 0 > single-exons51-57.distr.baseline
611 16:37 genezilla/get-duration-distr.pl single-exons51-57.fasta 50 2 12 10 1.08 > single-exons51-57.distr ; xgraph -lw 2 single-exons51-57.distr single-exons51-57.distr.baseline
613 16:39 genezilla/get-duration-distr.pl initial-exons51-57.fasta 50 0 0 0 0 > initial-exons51-57.distr.baseline
614 16:39 genezilla/get-duration-distr.pl initial-exons51-57.fasta 50 4 1 0 0 > initial-exons51-57.distr ; xgraph initial-exons51-57.distr initial-exons51-57.distr.baseline
615 16:40 genezilla/get-duration-distr.pl internal-exons51-57.fasta 50 0 0 0 0 > internal-exons51-57.distr.baseline
628 16:46 genezilla/get-duration-distr.pl internal-exons51-57.fasta 25 4 1 1 1.02 > internal-exons51-57.distr ; xgraph internal-exons51-57.distr internal-exons51-57.distr.baseline
630 16:47 genezilla/get-duration-distr.pl final-exons51-57.fasta 25 0 0 0 0 > final-exons51-57.distr.baseline
631 16:47 genezilla/get-duration-distr.pl final-exons51-57.fasta 25 4 4 3 1.01 > final-exons51-57.distr ; xgraph -lw 2 final-exons51-57.distr final-exons51-57.distr.baseline
632 16:48 cd ../iso57-100
634 16:48 genezilla/get-duration-distr.pl single-exons57-100.fasta 50 0 0 0 0 > single-exons57-100.distr.baseline
646 17:42 genezilla/get-duration-distr.pl single-exons57-100.fasta 200 2 12 2 1.01 > single-exons57-100.distr ; xgraph -lw 2 single-exons57-100.distr single-exons57-100.distr.baseline
648 17:43 genezilla/get-duration-distr.pl initial-exons57-100.fasta 50 0 0 0 0 > initial-exons57-100.distr.baseline
659 17:47 genezilla/get-duration-distr.pl initial-exons57-100.fasta 25 4 4 1 1.01 > initial-exons57-100.distr ; xgraph initial-exons57-100.distr initial-exons57-100.distr.baseline
661 17:49 genezilla/get-duration-distr.pl internal-exons57-100.fasta 25 0 0 0 0 > internal-exons57-100.distr.baseline
671 17:51 genezilla/get-duration-distr.pl internal-exons57-100.fasta 25 4 1 1 0.97 > internal-exons57-100.distr ; xgraph -lw 2 internal-exons57-100.distr internal-exons57-100.distr.baseline
673 17:52 genezilla/get-duration-distr.pl final-exons57-100.fasta 25 0 0 0 0 > final-exons57-100.distr.baseline
677 17:53 genezilla/get-duration-distr.pl final-exons57-100.fasta 25 4 4 3 1.026 > final-exons57-100.distr ; xgraph -lw 2 final-exons57-100.distr final-exons57-100.distr.baseline
679 17:55 cd ..
680 17:55 mkdir iso0-100
684 17:56 cd iso0-43
685 17:56 cat initial-exons0-43.fasta internal-exons0-43.fasta final-exons0-43.fasta single-exons0-43.fasta > all-exons0-43.fasta
686 17:56 cd ../iso43-51
687 17:57 cat initial-exons43-51.fasta internal-exons43-51.fasta final-exons43-51.fasta single-exons43-51.fasta > all-exons43-51.fasta
688 17:57 cd ../iso51-57
689 17:57 cat initial-exons51-57.fasta internal-exons51-57.fasta final-exons51-57.fasta single-exons51-57.fasta > all-exons51-57.fasta
690 17:57 cd ../iso57-100
691 17:57 cat initial-exons57-100.fasta internal-exons57-100.fasta final-exons57-100.fasta single-exons57-100.fasta > all-exons57-100.fasta
692 17:58 cd ../iso0-100
693 17:58 cat ../iso0-43/all-exons0-43.fasta ../iso43-51/all-exons43-51.fasta ../iso51-57/all-exons51-57.fasta ../iso57-100/all-exons57-100.fasta > all-exons0-100.fasta
695 17:59 genezilla/train-content-sensor -o 5 -s 175 3PIMM all-exons0-100.fasta ../iso0-43/non-initial-exons0-43.fasta exons0-100 1.0 INITIAL-EXON
696 18:00 ln -s ~/GF/genezilla
697 18:00 genezilla/train-content-sensor -o 5 -s 175 3PIMM all-exons0-100.fasta ../iso0-43/non-initial-exons0-43.fasta exons0-100 1.0 INITIAL-EXON
698 7:49 cd ..
700 7:49 cd ../iso0-43
701 7:50 cd iso0-43
703 7:50 genezilla/train-content-sensor -o 5 -s 175 3PIMM all-exons0-43.fasta non-initial-exons0-43.fasta exons0-43 1.0 INITIAL-EXON
704 7:51 cd ../iso43-51
706 7:51 genezilla/train-content-sensor -o 5 -s 175 3PIMM all-exons43-51.fasta non-initial-exons43-51.fasta exons43-51 1.0 INITIAL-EXON
707 7:51 cd ../iso51-57
709 7:52 genezilla/train-content-sensor -o 5 -s 175 3PIMM all-exons51-57.fasta non-initial-exons51-57.fasta exons51-57 1.0 INITIAL-EXON
710 7:52 cd ../iso57-100
711 7:52 genezilla/train-content-sensor -o 5 -s 175 3PIMM all-exons57-100.fasta non-initial-exons57-100.fasta exons57-100 1.0 INITIAL-EXON
712 7:53 cd ../iso43-100
715 7:53 cat ../iso43-51/all-exons43-51.fasta ../iso51-57/all-exons51-57.fasta ../iso57-100/all-exons57-100.fasta > exons43-100.fasta
716 7:53 mv exons43-100.fasta all-exons43-100.fasta
717 7:54 genezilla/train-content-sensor -o 5 -s 175 3PIMM all-exons43-100.fasta ../iso0-43/non-initial-exons0-43.fasta exons43-100 1.0 INITIAL-EXON
719 7:54 genezilla/train-content-sensor -o 5 -s 175 3PIMM all-exons43-100.fasta ../iso0-43/non-initial-exons0-43.fasta exons43-100 1.0 INITIAL-EXON
721 7:55 compile-markov-chain exons43-100.model
722 7:55 cd ../iso0-43
723 7:55 compile-markov-chain exons0-43.model
724 7:55 cd ../iso43-51
725 7:55 compile-markov-chain exons43-51.model
726 7:55 cd ../iso51-57
727 7:55 compile-markov-chain exons51-57.model
728 7:56 cd ../iso57-100
729 7:56 compile-markov-chain exons57-100.model
730 7:56 cd ../iso0-100
731 7:56 compile-markov-chain exons0-100.model
733 7:57 cd ../iso0-43
735 7:58 genezilla/train-content-sensor -o 5 -s 175 IMM introns0-43.fasta ../iso0-43/non-introns0-43.fasta introns0-43 1.0 INTRON
736 7:58 compile-markov-chain introns0-43.model
737 7:58 cd ../iso43-51
738 7:59 genezilla/train-content-sensor -o 5 -s 175 IMM introns43-51.fasta ../iso0-43/non-introns0-43.fasta introns43-51 1.0 INTRON
739 7:59 compile-markov-chain introns43-51.model
740 7:59 cd ../iso51-57
741 7:59 genezilla/train-content-sensor -o 5 -s 175 IMM introns51-57.fasta ../iso0-43/non-introns0-43.fasta introns51-57 1.0 INTRON
742 8:00 compile-markov-chain introns51-57.model
743 8:00 cd ../iso57-100
744 8:00 genezilla/train-content-sensor -o 5 -s 175 IMM introns57-100.fasta ../iso0-43/non-introns0-43.fasta introns57-100 1.0 INTRON
745 8:01 cd ../iso43-100
746 8:01 cat ../iso43-51/introns43-51.fasta ../iso51-57/introns51-57.fasta ../iso57-100/introns57-100.fasta > introns43-100.fasta
747 8:01 genezilla/train-content-sensor -o 5 -s 175 IMM introns43-100.fasta ../iso0-43/non-introns0-43.fasta introns43-100 1.0 INTRON
748 8:02 cd ../iso0-100
749 8:03 cat ../iso0-43/introns0-43.fasta ../iso43-51/introns43-51.fasta ../iso51-57/introns51-57.fasta ../iso57-100/introns57-100.fasta > introns0-100.fasta
750 8:03 genezilla/train-content-sensor -o 5 -s 175 IMM introns0-100.fasta ../iso0-43/non-introns0-43.fasta introns0-100 1.0 INTRON
751 8:03 compile-markov-chain introns0-100.model
754 8:07 cd ../iso43-100
755 8:07 compile-markov-chain introns43-100.model
757 8:07 cd ../iso0-43
759 8:08 genezilla/train-content-sensor -o 5 -s 175 IMM intergenic0-43.fasta ../iso0-43/non-intergenic0-43.fasta intergenic0-43 1.0 INTERGENIC
760 8:08 compile-markov-chain intergenic0-43.model
761 8:08 cd ../iso51-57
762 8:09 genezilla/train-content-sensor -o 5 -s 175 IMM intergenic51-57.fasta ../iso0-43/non-intergenic0-43.fasta intergenic51-57 1.0 INTERGENIC ; compile-markov-chain intergenic51-57.model
763 8:09 cd ../iso43-51
764 8:09 genezilla/train-content-sensor -o 5 -s 175 IMM intergenic43-51.fasta ../iso0-43/non-intergenic0-43.fasta intergenic43-51 1.0 INTERGENIC ; compile-markov-chain intergenic43-51.model
765 8:10 cd ../iso57-100
766 8:10 genezilla/train-content-sensor -o 5 -s 175 IMM intergenic57-100.fasta ../iso0-43/non-intergenic0-43.fasta intergenic57-100 1.0 INTERGENIC ; compile-markov-chain intergenic57-100.model
767 8:10 cd ../iso0-100
768 8:11 cat ../iso0-43/intergenic0-43.fasta ../iso43-51/intergenic43-51.fasta ../iso51-57/intergenic51-57.fasta ../iso57-100/intergenic57-100.fasta > intergenic0-100.fasta
769 8:12 genezilla/train-content-sensor -o 5 -s 175 IMM intergenic0-100.fasta ../iso0-43/non-intergenic0-43.fasta intergenic0-100 1.0 INTERGENIC ; compile-markov-chain intergenic0-100.model
770 8:12 cd ../iso43-100
771 8:12 cat ../iso43-51/intergenic43-51.fasta ../iso51-57/intergenic51-57.fasta ../iso57-100/intergenic57-100.fasta > intergenic43-100.fasta
772 8:12 genezilla/train-content-sensor -o 5 -s 175 IMM intergenic43-100.fasta ../iso0-43/non-intergenic0-43.fasta intergenic43-100 1.0 INTERGENIC ; compile-markov-chain intergenic43-100.model
773 8:13 cd ..
775 8:13 cd iso0-43
777 8:14 genezilla/train-content-sensor -o 5 -s 175 IMM five-prime-UTR0-43.fasta ../iso0-43/non-intergenic0-43.fasta five-prime-UTR0-43 1.0 FIVE-PRIME-UTR ; compile-markov-chain five-prime-UTR0-43.model
778 8:14 cd ../iso43-51
779 8:15 genezilla/train-content-sensor -o 5 -s 175 IMM five-prime-UTR43-51.fasta ../iso0-43/non-intergenic0-43.fasta five-prime-UTR43-51 1.0 FIVE-PRIME-UTR ; compile-markov-chain five-prime-UTR43-51.model
780 8:15 cd ../iso51-57
781 8:15 genezilla/train-content-sensor -o 5 -s 175 IMM five-prime-UTR51-57.fasta ../iso0-43/non-intergenic0-43.fasta five-prime-UTR51-57 1.0 FIVE-PRIME-UTR ; compile-markov-chain five-prime-UTR51-57.model
782 8:15 cd ../iso57-100
783 8:15 genezilla/train-content-sensor -o 5 -s 175 IMM five-prime-UTR557-100.fasta ../iso0-43/non-intergenic0-43.fasta five-prime-UTR57-100 1.0 FIVE-PRIME-UTR ; compile-markov-chain five-prime-UTR57-100.model
784 8:16 genezilla/train-content-sensor -o 5 -s 175 IMM five-prime-UTR57-100.fasta ../iso0-43/non-intergenic0-43.fasta five-prime-UTR57-100 1.0 FIVE-PRIME-UTR ; compile-markov-chain five-prime-UTR57-100.model
785 8:16 cd ../iso0-100
786 8:16 cat ../iso0-43/five-prime-UTR0-43.fasta ../iso43-51/five-prime-UTR43-51.fasta ../iso51-57/five-prime-UTR51-57.fasta ../iso57-100/five-prime-UTR57-100.fasta > five-prime-UTR0-100.fasta
787 8:17 genezilla/train-content-sensor -o 5 -s 175 IMM five-prime-UTR0-100.fasta ../iso0-43/non-intergenic0-43.fasta five-prime-UTR0-100 1.0 FIVE-PRIME-UTR ; compile-markov-chain five-prime-UTR0-100.model
788 8:17 cd ../iso43-100
789 8:17 cat ../iso43-51/five-prime-UTR43-51.fasta ../iso51-57/five-prime-UTR51-57.fasta ../iso57-100/five-prime-UTR57-100.fasta > five-prime-UTR43-100.fasta
790 8:17 genezilla/train-content-sensor -o 5 -s 175 IMM five-prime-UTR43-100.fasta ../iso0-43/non-intergenic0-43.fasta five-prime-UTR43-100 1.0 FIVE-PRIME-UTR ; compile-markov-chain five-prime-UTR43-100.model
791 8:18 cd ../iso0-43
792 8:18 genezilla/train-content-sensor -o 5 -s 175 IMM three-prime-UTR0-43.fasta ../iso0-43/non-intergenic0-43.fasta three-prime-UTR0-43 1.0 THREE-PRIME-UTR ; compile-markov-chain three-prime-UTR0-43.model
793 8:18 cd ../iso43-51
794 8:19 genezilla/train-content-sensor -o 5 -s 175 IMM three-prime-UTR43-51.fasta ../iso0-43/non-intergenic0-43.fasta three-prime-UTR43-51 1.0 THREE-PRIME-UTR ; compile-markov-chain three-prime-UTR43-51.model
795 8:19 cd ../iso51-57
796 8:19 genezilla/train-content-sensor -o 5 -s 175 IMM three-prime-UTR51-57.fasta ../iso0-43/non-intergenic0-43.fasta three-prime-UTR51-57 1.0 THREE-PRIME-UTR ; compile-markov-chain three-prime-UTR51-57.model
797 8:19 cd ../iso57-100
798 8:20 genezilla/train-content-sensor -o 5 -s 175 IMM three-prime-UTR57-100.fasta ../iso0-43/non-intergenic0-43.fasta three-prime-UTR57-100 1.0 THREE-PRIME-UTR ; compile-markov-chain three-prime-UTR57-100.model
799 8:20 cd ../iso0-100
800 8:21 cat ../iso0-43/three-prime-UTR0-43.fasta ../iso43-51/three-prime-UTR43-51.fasta ../iso51-57/three-prime-UTR51-57.fasta ../iso57-100/three-prime-UTR57-100.fasta > three-prime-UTR0-100.fasta
801 8:21 genezilla/train-content-sensor -o 5 -s 175 IMM three-prime-UTR0-100.fasta ../iso0-43/non-intergenic0-43.fasta three-prime-UTR0-100 1.0 THREE-PRIME-UTR ; compile-markov-chain three-prime-UTR0-100.model
802 8:21 cd ../iso43-100
803 8:21 cat ../iso43-51/three-prime-UTR43-51.fasta ../iso51-57/three-prime-UTR51-57.fasta ../iso57-100/three-prime-UTR57-100.fasta > three-prime-UTR43-100.fasta
804 8:22 genezilla/train-content-sensor -o 5 -s 175 IMM three-prime-UTR43-100.fasta ../iso0-43/non-intergenic0-43.fasta three-prime-UTR43-100 1.0 THREE-PRIME-UTR ; compile-markov-chain three-prime-UTR43-100.model
805 8:23 cd ../iso0-100
806 8:24 cat intergenic0-100.fasta introns0-100.fasta five-prime-UTR0-100.fasta three-prime-UTR0-100.fasta > noncoding0-100.fasta
807 8:24 genezilla/train-content-sensor -o 5 -s 175 IMM noncoding0-100.fasta ../iso0-43/non-intergenic0-43.fasta noncoding0-100 1.0 INTERGENIC ; compile-markov-chain noncoding0-100.model
808 8:25 cd ../iso0-43
809 8:25 cat intergenic0-43.fasta introns0-43.fasta five-prime-UTR0-43.fasta three-prime-UTR0-43.fasta > noncoding0-43.fasta
810 8:25 genezilla/train-content-sensor -o 5 -s 175 IMM noncoding0-43.fasta ../iso0-43/non-intergenic0-43.fasta noncoding0-43 1.0 INTERGENIC ; compile-markov-chain noncoding0-43.model
811 8:30 cd ../iso43-51
812 8:31 cat intergenic43-51.fasta introns43-51.fasta five-prime-UTR43-51.fasta three-prime-UTR43-51.fasta > noncoding43-51.fasta
813 8:31 genezilla/train-content-sensor -o 5 -s 175 IMM noncoding43-51.fasta ../iso0-43/non-intergenic0-43.fasta noncoding43-51 1.0 INTERGENIC ; compile-markov-chain noncoding43-51.model
815 8:31 cd ../iso51-57
816 8:32 cat intergenic51-57.fasta introns51-57.fasta five-prime-UTR51-57.fasta three-prime-UTR51-57.fasta > noncoding51-57.fasta
817 8:32 genezilla/train-content-sensor -o 5 -s 175 IMM noncoding51-57.fasta ../iso0-43/non-intergenic0-43.fasta noncoding51-57 1.0 INTERGENIC ; compile-markov-chain noncoding51-57.model
818 8:32 cd ../iso57-100
819 8:33 cat intergenic57-100.fasta introns57-100.fasta five-prime-UTR57-100.fasta three-prime-UTR57-100.fasta > noncoding57-100.fasta
820 8:33 genezilla/train-content-sensor -o 5 -s 175 IMM noncoding57-100.fasta ../iso0-43/non-intergenic0-43.fasta noncoding57-100 1.0 INTERGENIC ; compile-markov-chain noncoding57-100.model
822 8:33 cd ../iso43-100
823 8:34 cat intergenic43-100.fasta introns43-100.fasta five-prime-UTR43-100.fasta three-prime-UTR43-100.fasta > noncoding43-100.fasta
824 8:34 genezilla/train-content-sensor -o 5 -s 175 IMM noncoding43-100.fasta ../iso0-43/non-intergenic0-43.fasta noncoding43-100 1.0 INTERGENIC ; compile-markov-chain noncoding43-100.model
825 8:36 cd ../iso0-43
830 8:36 genezilla/get-trans-distr.pl iso0-43.gff > iso0-43.trans
831 8:37 cd ../iso43-51
832 8:37 genezilla/get-trans-distr.pl iso43-51.gff > iso43-51.trans
833 8:37 cd ../iso51-57
834 8:37 genezilla/get-trans-distr.pl iso51-57.gff > iso51-57.trans
835 8:37 cd ../iso57-100
836 8:38 genezilla/get-trans-distr.pl iso57-100.gff > iso57-100.trans
837 8:38 cd ../iso0-100
839 8:38 genezilla/get-trans-distr.pl ../iso0-100.gff > iso0-100.trans
840 8:38 cd ../iso43-100
843 8:39 cat ../iso43-51/iso43-51.gff ../iso51-57/iso51-57.gff ../iso57-100/iso57-100.gff > iso43-100.gff
844 8:39 genezilla/get-trans-distr.pl ../iso43-100.gff > iso43-100.trans
845 8:39 genezilla/get-trans-distr.pl iso43-100.gff > iso43-100.trans
846 8:40 cd ../iso0-43
849 8:41 genezilla/train-signal.pl WMM start-codons0-43.fasta non-start-codons0-43.fasta start-codons0-43 1 ATG 6 3 12 0.99 1 175 0 0
850 8:42 cd ../iso43-51
851 8:42 genezilla/train-signal.pl WMM start-codons43-51.fasta non-start-codons43-51.fasta start-codons43-51 1 ATG 6 3 12 0.99 1 175 0 0
852 8:42 cd ../iso51-57
853 8:43 genezilla/train-signal.pl WMM start-codons51-57.fasta non-start-codons51-57.fasta start-codons51-57 1 ATG 6 3 12 0.99 1 175 0 0
854 8:43 cd ../iso57-100
855 8:43 genezilla/train-signal.pl WMM start-codons57-100.fasta non-start-codons57-100.fasta start-codons57-100 1 ATG 6 3 12 0.99 1 175 0 0
856 8:43 cd ../iso43-100
857 8:43 genezilla/train-signal.pl WMM start-codons43-100.fasta non-start-codons43-100.fasta start-codons43-100 1 ATG 6 3 12 0.99 1 175 0 0
858 8:44 cat ../iso43-51/start-codons43-51.fasta ../iso51-57/start-codons51-57.fasta ../iso57-100/start-codons57-100.fasta > start-codons43-100.fasta
859 8:44 genezilla/train-signal.pl WMM start-codons43-100.fasta non-start-codons43-100.fasta start-codons43-100 1 ATG 6 3 12 0.99 1 175 0 0
860 8:44 cat ../iso43-51/non-start-codons43-51.fasta ../iso51-57/non-start-codons51-57.fasta ../iso57-100/non-start-codons57-100.fasta > non-start-codons43-100.fasta
861 8:44 genezilla/train-signal.pl WMM start-codons43-100.fasta non-start-codons43-100.fasta start-codons43-100 1 ATG 6 3 12 0.99 1 175 0 0
862 8:44 cd ../iso0-100
863 8:44 cat iso0-43/non-start-codons0-43.fasta ../iso43-51/non-start-codons43-51.fasta ../iso51-57/non-start-codons51-57.fasta ../iso57-100/non-start-codons57-100.fasta > non-start-codons0-100.fasta
864 8:45 cat ../iso0-43/non-start-codons0-43.fasta ../iso43-51/non-start-codons43-51.fasta ../iso51-57/non-start-codons51-57.fasta ../iso57-100/non-start-codons57-100.fasta > non-start-codons0-100.fasta
865 8:45 cat ../iso0-43/start-codons0-43.fasta ../iso43-51/start-codons43-51.fasta ../iso51-57/start-codons51-57.fasta ../iso57-100/start-codons57-100.fasta > start-codons0-100.fasta
866 8:45 genezilla/train-signal.pl WMM start-codons0-100.fasta non-start-codons0-100.fasta start-codons0-100 1 ATG 6 3 12 0.99 1 175 0 0
867 8:46 cd ../iso0-43
868 8:47 genezilla/train-signal.pl WAM stop-codons0-43.fasta non-stop-codons0-43.fasta stop-codons0-43 1 TAG 0 3 6 0.99 1 175 0 0
870 8:48 cd ../iso43-51
871 8:48 genezilla/train-signal.pl WAM stop-codons43-51.fasta non-stop-codons43-51.fasta stop-codons43-51 1 TAG 0 3 6 0.99 1 175 0 0
872 8:48 cd ../iso51-57
873 8:48 genezilla/train-signal.pl WAM stop-codons51-57.fasta non-stop-codons51-57.fasta stop-codons51-57 1 TAG 0 3 6 0.99 1 175 0 0
874 8:48 cd ../iso57-100
875 8:49 genezilla/train-signal.pl WAM stop-codons57-100.fasta non-stop-codons57-100.fasta stop-codons57-100 1 TAG 0 3 6 0.99 1 175 0 0
876 8:49 cd ../iso43-100
877 8:49 cat ../iso43-51/stop-codons43-51.fasta ../iso51-57/stop-codons51-57.fasta ../iso57-100/stop-codons57-100.fasta > stop-codons43-100.fasta
878 8:50 genezilla/train-signal.pl WAM stop-codons43-100.fasta non-stop-codons43-100.fasta stop-codons43-100 1 TAG 0 3 6 0.99 1 175 0 0
879 8:50 cat ../iso43-51/non-stop-codons43-51.fasta ../iso51-57/non-stop-codons51-57.fasta ../iso57-100/non-stop-codons57-100.fasta > non-stop-codons43-100.fasta
880 8:50 genezilla/train-signal.pl WAM stop-codons43-100.fasta non-stop-codons43-100.fasta stop-codons43-100 1 TAG 0 3 6 0.99 1 175 0 0
881 8:50 cd ../iso0-100
882 8:51 cat ../iso0-43/non-stop-codons0-43.fasta ../iso43-51/non-stop-codons43-51.fasta ../iso51-57/non-stop-codons51-57.fasta ../iso57-100/non-stop-codons57-100.fasta > non-stop-codons0-100.fasta
883 8:51 cat ../iso0-43/stop-codons0-43.fasta ../iso43-51/stop-codons43-51.fasta ../iso51-57/stop-codons51-57.fasta ../iso57-100/stop-codons57-100.fasta > stop-codons0-100.fasta
884 8:51 genezilla/train-signal.pl WAM stop-codons0-100.fasta non-stop-codons0-100.fasta stop-codons0-100 1 TAG 0 3 6 0.99 1 175 0 0
888 8:55 cat ../iso0-43/donors0-43.fasta ../iso43-51/donors43-51.fasta ../iso51-57/donors51-57.fasta ../iso57-100/donors57-100.fasta > donors0-100.fasta
889 8:55 genezilla/train-mdd.pl WMM donors0-100.fasta non-donors0-100.fasta donors0-100 1 GT 3 2 9 1.00 0 175 5 0 0
890 8:55 cat ../iso0-43/non-donors0-43.fasta ../iso43-51/non-donors43-51.fasta ../iso51-57/non-donors51-57.fasta ../iso57-100/non-donors57-100.fasta > non-donors0-100.fasta
891 8:55 genezilla/train-mdd.pl WMM donors0-100.fasta non-donors0-100.fasta donors0-100 1 GT 3 2 9 1.00 0 175 5 0 0
892 8:59 genezilla/train-mdd.pl WMM donors0-100.fasta non-donors0-100.fasta donors0-100 1 GT 3 2 9 1.00 0 175 3 0 0
893 9:00 cd ../iso43-100
894 9:00 cat ../iso43-51/non-donors43-51.fasta ../iso51-57/non-donors51-57.fasta ../iso57-100/non-donors57-100.fasta > non-donors43-100.fasta
895 9:01 cat ../iso43-51/donors43-51.fasta ../iso51-57/donors51-57.fasta ../iso57-100/donors57-100.fasta > donors43-100.fasta
896 9:01 genezilla/train-mdd.pl WMM donors43-100.fasta non-donors43-100.fasta donors43-100 1 GT 3 2 9 1.00 0 175 3 0 0
897 9:03 cd ../iso0-43
898 9:03 genezilla/train-mdd.pl WMM donors0-43.fasta non-donors0-43.fasta donors0-43 1 GT 3 2 9 1.00 0 175 3 0 0
899 9:04 cd ../iso43-51
900 9:04 genezilla/train-mdd.pl WMM donors43-51.fasta non-donors43-51.fasta donors43-51 1 GT 3 2 9 1.00 0 175 3 0 0
901 9:05 cd ../iso51-57
902 9:05 genezilla/train-mdd.pl WMM donors51-57.fasta non-donors51-57.fasta donors51-57 1 GT 3 2 9 1.00 0 175 3 0 0
903 9:05 cd ../iso57-100
904 9:06 genezilla/train-mdd.pl WMM donors57-100.fasta non-donors57-100.fasta donors57-100 1 GT 3 2 9 1.00 0 175 3 0 0
906 9:10 cd ../iso0-100
908 9:11 cat ../iso0-43/acceptors0-43.fasta ../iso43-51/acceptors43-51.fasta ../iso51-57/acceptors51-57.fasta ../iso57-100/acceptors57-100.fasta > acceptors0-100.fasta
909 9:12 cat ../iso0-43/non-acceptors0-43.fasta ../iso43-51/non-acceptors43-51.fasta ../iso51-57/non-acceptors51-57.fasta ../iso57-100/non-acceptors57-100.fasta > non-acceptors0-100.fasta
910 9:12 train-branch-acceptor.pl acceptors0-100.fasta non-acceptors0-100.fasta branchpoint 1 27 7 23 1.0 2 2 175 3 0.4
911 9:14 train-branch-acceptor.pl acceptors0-100.fasta non-acceptors0-100.fasta branchpoint 1 27 7 23 1.0 2 2 175 0 0
912 9:15 cd ../iso43-100
913 9:15 cat ../iso43-51/non-acceptors43-51.fasta ../iso51-57/non-acceptors51-57.fasta ../iso57-100/non-acceptors57-100.fasta > non-acceptors43-100.fasta
914 9:15 cat ../iso43-51/acceptors43-51.fasta ../iso51-57/acceptors51-57.fasta ../iso57-100/acceptors57-100.fasta > acceptors43-100.fasta
915 9:15 train-branch-acceptor.pl acceptors43-100.fasta non-acceptors43-100.fasta branchpoint 1 27 7 23 1.0 2 2 175 0 0
916 9:16 cd ../iso0-43
917 9:16 train-branch-acceptor.pl acceptors0-43.fasta non-acceptors0-43.fasta branchpoint 1 27 7 23 1.0 2 2 175 0 0
918 9:16 cd ../iso43-51
919 9:16 train-branch-acceptor.pl acceptors43-51.fasta non-acceptors43-51.fasta branchpoint 1 27 7 23 1.0 2 2 175 0 0
920 9:17 cd ../iso51-57
921 9:17 train-branch-acceptor.pl acceptors51-57.fasta non-acceptors51-57.fasta branchpoint 1 27 7 23 1.0 2 2 175 0 0
922 9:17 cd ../iso57-100
923 9:17 train-branch-acceptor.pl acceptors57-100.fasta non-acceptors57-100.fasta branchpoint 1 27 7 23 1.0 2 2 175 0 0
