| 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 | |
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| 5 | #Please insert subtopic references (line starts with keyword SUB) |
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| 6 | SUB sel_box.hlp |
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| 7 | |
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| 8 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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| 9 | |
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| 10 | #************* Title of helpfile !! and start of real helpfile strunk******** |
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| 11 | TITLE Potential Probe Targets |
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| 12 | |
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| 13 | OCCURRENCE ARB_NT/ETC/Probe Design/PROBE DESIGN/PD RESULT |
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| 14 | |
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| 15 | DESCRIPTION The 'PD RESULT' window is displayed automatically after |
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| 16 | finishing the probe target searching or manually by pressing the |
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| 17 | 'RESULT' button of the 'PROBE DESIGN' window. |
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| 18 | |
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| 19 | The parameters defined by in the 'PROBE DESIGN' window are |
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| 20 | listed in the first line of the display area of the 'PD |
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| 21 | RESULT' window. |
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| 22 | |
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| 23 | The target and probe sequences are given in the first and last |
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| 24 | columns of the display area, respectively. |
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| 25 | |
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| 26 | The length of the proposed probe is given in column 2. |
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| 27 | |
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| 28 | Columns 3 and 4 indicate the 5'-positions of the target sites |
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| 29 | within the alignment and the E.coli sequence, |
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| 30 | respectively |
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| 31 | |
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| 32 | The number of species targeted (perfectly paired) by the probe |
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| 33 | is given in column 5. |
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| 34 | |
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| 35 | The G+C contents and predicted dissociation temperatures (4xGC + |
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| 36 | 2xAT) are listed in columns 6 and 7, respectively. |
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| 37 | |
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| 38 | The numbers of the next columns (from left to right) indicated |
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| 39 | how many non-target species would be detected by the |
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| 40 | particular probe if the temperature would be gradually |
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| 41 | lowered. |
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| 42 | |
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| 43 | !!! The columns do only represent virtual temperature |
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| 44 | shifts and cannot be assigned to degree centigrade!!! |
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| 45 | |
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| 46 | To write the results to an ascii file press the 'SAVE' button |
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| 47 | to display the 'SELECTION BOX' window. |
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| 48 | |
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| 49 | The 'Auto match' toggle has the same meaning as in LINK{probematch.hlp}. |
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| 50 | |
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| 51 | SECTION SORTING |
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| 52 | |
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| 53 | The program brings the best probes to the front of the list. |
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| 54 | Best means the product |
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| 55 | |
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| 56 | group_hits * (min. mismatches to non group sp.) |
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| 57 | |
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| 58 | It does not take G+C, temperature or ECOLI position into account. |
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| 59 | It is up to the user to study the list carefully and choose his |
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| 60 | candidates. ( In our lab we often found the 20th probe the best ). |
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| 61 | |
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| 62 | |
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| 63 | NOTES None |
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| 64 | |
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| 65 | EXAMPLES None |
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| 66 | |
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| 67 | WARNINGS None |
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| 68 | |
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| 69 | BUGS No bugs known |
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