Primer Design/Search Parameters

ARB_NT/ETC/Primer Design

left/right position: specifies the start of primer ranges (leftmost base position) [right.min > left.min]

left/right number of bases specifies how many bases a primer range includes

primer length: number of bases within a primer [length > 0]

primer distance: min/max number of bases between leftmost base in left primer and rightmost base in right primer

G+C ratio: range of GC-ratio of primers in percent (countG+countC / countBases * 100)

temperature: range of temperature of primers (4*(countG+countC) + 2*(countA+countT))

minimal distance to next match of primer:
if a primer is found again outside this range it is ignored
example: primerpos        100
         min.dist          50
         2nd occurrence    30 => primer remains in list
         3rd occurrence   140 => primer is removed from list

expand IUPAC-codes: switches expansion of IUPAC-codes on/off example: TTRC is expanded to TTAC and TTGC

maximal number of results: how many possible pairs you want?

G+C-factor / temperature-factor: weight of GC / temperature while evaluation of possible primerpairs

written by Wolfram Foerster 2001

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No bugs known