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Last change
on this file was
19532,
checked in by westram, 4 months ago
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- reintegrates 'help' into 'trunk'
- tweak arb documentation:
- automatically link
- ticket references to arb
 tracker (only affects html version).
- found URLs.
- page titles
- warn about long titles.
- introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
- increase allowed length (limited by subwindow width).
- cleanup header sections in all helpfiles.
- fix and/or update several help files.
- document syntax of help sources.
- build issues:
- when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
- remove output files on error (including files below ARBHOME/lib).
- pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
- moves Tree admin + NDS menu entries to top of menu
- adds: log:branches/help@18783:19531
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Property svn:eol-style set to
native
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Property svn:keywords set to
Author Date Id Revision
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File size:
1.2 KB
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| 1 | # main topics: |
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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 | # sub topics: |
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| 6 | #SUB subtopic.hlp |
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| 7 | |
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| 8 | # format described in ../help.readme |
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| 9 | |
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| 10 | |
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| 11 | TITLE Design Sequencing Primers |
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| 12 | |
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| 13 | OCCURRENCE ARB_NT/Probes/Design Sequencing Primers |
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| 14 | |
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| 15 | DESCRIPTION This module will search for primers for all positions. |
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| 16 | |
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| 17 | The best result is one primer for all (marked) taxa, |
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| 18 | the worst case are n primers for n taxa. |
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| 19 | |
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| 20 | * does only search in marked sequences. |
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| 21 | * sequences need to be aligned. |
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| 22 | |
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| 23 | Searches for sections in alignment which require the lowest number |
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| 24 | of primer combinations. |
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| 25 | You have to specify the maximum allowed number of different primers. |
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| 26 | Specify '1' to report only primers valid for all marked species. |
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| 27 | |
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| 28 | The module outputs a list of primer candidates, |
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| 29 | probably outputs hundreds of pages. |
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| 30 | Checking these primers requires a lot of manual work. |
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| 31 | |
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| 32 | Press ctrl-C to abort the program. |
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| 33 | |
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| 34 | SECTION Field experience |
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| 35 | |
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| 36 | Bad sequences confuse the algorithm. |
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| 37 | Workaround: unmark them. |
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| 38 | |
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| 39 | NOTES None |
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| 40 | |
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| 41 | EXAMPLES None |
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| 42 | |
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| 43 | WARNINGS None |
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| 44 | |
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| 45 | BUGS No bugs known |
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