| 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/Probes/Design Probes/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 few lines of the 'PD RESULT' window. |
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| 21 | |
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| 22 | |
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| 23 | Description of single display columns: |
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| 24 | |
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| 25 | Column contains |
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| 26 | |
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| 27 | Target the target sequence of the designed probe |
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| 28 | le length of designed probe |
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| 29 | apos absolute 5'-position of the target sites |
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| 30 | (most often targeted position) |
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| 31 | ecol ecoli-relative position |
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| 32 | qual a probe quality indicator (see below) |
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| 33 | grps groupsize (number of perfect hits in target-species) |
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| 34 | G+C G+C content |
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| 35 | temp predicted dissociation temperature (4GC+2AT) |
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| 36 | Probe the designed probe sequence |
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| 37 | |
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| 38 | The numbers of the next columns (from left to right) indicates how many |
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| 39 | non-target species would be detected by this probe if the temperature would |
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| 40 | be gradually lowered ('_' means no hits). |
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| 41 | |
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| 42 | The columns do only represent virtual temperature shifts and cannot be |
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| 43 | assigned to degree centigrade! |
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| 44 | |
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| 45 | To write the results to an ascii file press the 'SAVE' button to display |
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| 46 | the 'SELECTION BOX' window. |
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| 47 | |
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| 48 | The 'Auto match' toggle has the same meaning as in LINK{probematch.hlp}. |
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| 49 | |
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| 50 | SECTION SORTING |
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| 51 | |
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| 52 | The probes are sorted by quality. The quality tries to reflect how good |
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| 53 | each probe separates between target- and non-target group. |
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| 54 | |
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| 55 | Therefore it detects the column COL in the decrease-temparature-list, |
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| 56 | where more than twice as much non-target species would get hitten, |
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| 57 | than mishits (i.e. non-group hits) were encountered by matching the probe. |
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| 58 | |
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| 59 | Using that column the quality is calculated using the formula |
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| 60 | |
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| 61 | 1000 |
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| 62 | quality = groupsize * COL + ------------------ |
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| 63 | 1000 + hits[COL] |
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| 64 | |
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| 65 | where: |
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| 66 | * COL is in range 0 .. 19 |
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| 67 | * mishits = probehits - groupsize |
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| 68 | * probehits = number of hits reported by probe match (zero mismatches) |
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| 69 | * COL is lowest column where: hits[COL] > 2*mishits |
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| 70 | * if no column matches the criterion above, COL=19 is used |
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| 71 | |
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| 72 | Probes with equal qualities are sorted by absolute position and |
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| 73 | then alphabetically. It does not take G+C content, temperature |
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| 74 | or ECOLI position into account. |
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| 75 | |
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| 76 | It is up to the user to study the list carefully and choose his |
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| 77 | candidates. In our lab we often found the 20th probe was the best. |
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| 78 | |
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| 79 | |
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| 80 | NOTES None |
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| 81 | |
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| 82 | EXAMPLES None |
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| 83 | |
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| 84 | WARNINGS None |
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| 85 | |
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| 86 | BUGS No bugs known |
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