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Main topics: ARB: a Short Introduction Glossary Design Primers | Related topics: Primer Design/IUPAC codes
# Primer Design/Search Parameters OCCURRENCE DESCRIPTION NOTES EXAMPLES WARNINGS BUGS ## OCCURRENCE
### ARB_NT/ETC/Primer Design
## DESCRIPTION
### 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
## NOTES
### written by Wolfram Foerster 2001
## EXAMPLES
### None
## WARNINGS
### None
## BUGS
### No bugs known