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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)
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

  ..........


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