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BESTPAL empirical help
BestPal_empirical
calculates best palindrome for given rna sequence, and also a set suboptimal palindromes (sorted by energy)
Output example: ==== structure 1 ==== Start End Energy 24 996 -173.6 Helices: 29 24 - 25 AC 996 - 995 UG 31 - 33 UCA 991 - 989 AGU 36 - 38 UCA 984 - 982 AGU 42 - 43 GA 978 - 977 CU 45 - 52 UGAUCGAU 975 - 968 GCUAGCUA 55 - 65 CUAGCUAGCUG 962 - 952 GAUCGAUCGAU 68 - 69 AC 948 - 947 UG 74 - 78 UGAUC 943 - 939 GCUAG 176 - 178 GUG 937 - 935 UAC 185 - 189 GCUAC 928 - 924 CGAUG 214 - 225 GUCGUACGUAGC 918 - 907 UAGCAUGCAUCG 503 - 513 AUCGUACGUAC 906 - 896 UAGCAUGCAUG 526 - 528 CUC 891 - 889 GGG 531 - 538 UACGUACG 884 - 877 AUGCAUGC 539 - 543 UACGC 847 - 843 GUGUG 550 - 561 GCUACGUACGUG 835 - 824 CGAUGCAUGCAU 562 - 565 ACUG 806 - 803 UGAU 569 - 571 GCA 798 - 796 CGU 582 - 587 GUGCAU 793 - 788 UACGUA 593 - 596 CGAU 779 - 776 GCUA 598 - 602 ACUGU 770 - 766 UGAUG 608 - 620 UAGCAUGCAUCGA 760 - 748 AUCGUACGUAGCU 621 - 622 GC 741 - 740 CG 627 - 629 GGC 734 - 732 UCG 631 - 636 GUCAGC 727 - 722 UAGUCG 639 - 641 GGU 716 - 714 UCG 642 - 648 GCUACGU 705 - 699 CGAUGCA 660 - 665 UGAUCG 697 - 692 GCUAGU 670 - 672 UAG 686 - 684 AUC ==== structure 2 ==== Start End Energy 3 998 -172.1 Helices: 24 3 - 8 GUACUA 998 - 993 CAUGGU 12 - 14 GUG 988 - 986 CAU 23 - 24 CA 983 - 982 GU 28 - 32 UGAUC 979 - 975 GCUAG 45 - 52 UGAUCGAU 971 - 964 GCUAGCUA 55 - 65 CUAGCUAGCUG 958 - 948 GAUCGAUCGAU 74 - 78 UGAUC 943 - 939 GCUAG 178 - 180 GUG 937 - 935 UAC 185 - 189 GCUAC 928 - 924 CGAUG 214 - 225 GUCGUACGUAGC 918 - 907 UAGCAUGCAUCG 503 - 513 AUCGUACGUAC 906 - 896 UAGCAUGCAUG 526 - 528 CUC 891 - 889 GGG 531 - 538 UACGUACG 884 - 877 AUGCAUGC 539 - 543 UACGC 847 - 843 GUGUG 550 - 561 GCUACGUACGUG 835 - 824 CGAUGCAUGCAU 567 - 570 CUGC 816 - 813 GAUG 578 - 583 ACUAGU 806 - 801 UGAUCG 607 - 620 GUAGCAUGCAUCGA 798 - 785 CGUCGUACGUAGCU 626 - 628 CGG 783 - 781 GCU 631 - 636 GUCAGC 777 - 772 UAGUCG 641 - 643 UGC 771 - 769 AUG 698 - 709 UACGUAGCUAGU 768 - 757 AUGCAUCGAUCG 714 - 715 GC 754 - 753 CG 720 - 725 UAGCUG 743 - 738 AUCGAU .......... |
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