| 1 | #Please insert up references in the next lines (line starts with keyword UP) |
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| 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | UP primer_new.hlp |
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| 5 | |
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| 6 | #Please insert subtopic references (line starts with keyword SUB) |
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| 7 | SUB iupac-codes.hlp |
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| 8 | |
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| 9 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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| 10 | |
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| 11 | #************* Title of helpfile !! and start of real helpfile ******** |
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| 12 | TITLE Primer Design/Search Parameters |
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| 13 | |
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| 14 | OCCURRENCE ARB_NT/ETC/Primer Design |
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| 15 | |
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| 16 | DESCRIPTION left/right position: |
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| 17 | specifies the start of primer ranges |
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| 18 | (leftmost base position) |
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| 19 | [right.min > left.min] |
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| 20 | |
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| 21 | left/right number of bases |
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| 22 | specifies how many bases a primer range includes |
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| 23 | |
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| 24 | primer length: |
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| 25 | number of bases within a primer |
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| 26 | [length > 0] |
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| 27 | |
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| 28 | primer distance: |
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| 29 | min/max number of bases between leftmost base in left primer |
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| 30 | and rightmost base in right primer |
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| 31 | |
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| 32 | G+C ratio: |
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| 33 | range of GC-ratio of primers in percent |
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| 34 | (countG+countC / countBases * 100) |
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| 35 | |
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| 36 | temperature: |
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| 37 | range of temperature of primers |
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| 38 | (4*(countG+countC) + 2*(countA+countT)) |
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| 39 | |
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| 40 | |
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| 41 | minimal distance to next match of primer: |
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| 42 | if a primer is found again outside this range it is ignored |
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| 43 | example: primerpos 100 |
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| 44 | min.dist 50 |
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| 45 | 2nd occurrence 30 => primer remains in list |
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| 46 | 3rd occurrence 140 => primer is removed from list |
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| 47 | |
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| 48 | expand IUPAC-codes: |
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| 49 | switches expansion of IUPAC-codes on/off |
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| 50 | example: TTRC is expanded to TTAC and TTGC |
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| 51 | |
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| 52 | maximal number of results: |
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| 53 | how many possible pairs you want ? |
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| 54 | |
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| 55 | G+C-factor / temperature-factor: |
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| 56 | weight of GC / temperature while evaluation of |
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| 57 | possible primerpairs |
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| 58 | |
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| 59 | NOTES written by Wolfram Foerster 2001 |
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| 60 | |
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| 61 | EXAMPLES None |
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| 62 | |
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| 63 | WARNINGS None |
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| 64 | |
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| 65 | BUGS No bugs known |
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