BestPal_empirical
calculates best palindrome for given rna sequence, and also a set suboptimal palindromes (sorted by energy)
Method description:
First the complementary matrix is built, and all helixes are detected. The they are sorted by their stability. Then starting each structure with one of most stable helixes from sorted list (each time different from others), the program upgrades them with compatible helixes until adding new helix gives no stability growth or when there are no more compatible helixes. Best N structures are written to user-defined file.
BestPal_empirical parameters:
Number of structures in output - number of suboptimal structures for output
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
..........