Skip to main content

Table 3 Parameters derived from the SUP sequence representation

From: Selection of antisense oligonucleotides based on multiple predicted target mRNA structures

Parameter Definition
f NS Number of bases in single-stranded region
f NP Number of bases in double-stranded region
f PS Percentage of bases in single-stranded region to the length of ODN
f PP Percentage of bases in double-stranded region to the length of ODN
f CS Maximum length of consecutive subsequence in single-stranded region
f CP Maximum length of consecutive subsequence in base pairing
f 5S Maximum length of consecutive subsequence in single-stranded region counting from 5' terminal
f 5P Maximum length of consecutive subsequence in base pairing counting from 5' terminal
f 3S Maximum length of consecutive subsequence in single-stranded region counting from 3' terminal
f 3P Maximum length of consecutive subsequence in base pairing counting from 3' terminal
f SC Structure consistency, f S C = 1 n 1 i = 1 n 1 E ( S i , S i 1 ) MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGMbGzdaWgaaWcbaGaem4uamLaem4qameabeaakiabg2da9maalaaabaGaeGymaedabaGaemOBa4MaeyOeI0IaeGymaedaamaaqahabaGaemyrauKaeiikaGIaem4uam1aaSbaaSqaaiabdMgaPbqabaGccqGGSaalcqWGtbWudaWgaaWcbaGaemyAaKMaeyOeI0IaeGymaedabeaakiabcMcaPaWcbaGaemyAaKMaeyypa0JaeGymaedabaGaemOBa4MaeyOeI0IaeGymaedaniabggHiLdaaaa@4994@ , where E ( x , y ) = { 1 , x = y ' U ' 0 , x = ' U ' , o r y = ' U ' -1 x y , x ' S ' , y ' P ' MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=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@6622@