source: branches/species/HELP_SOURCE/source/probeadmin.hlp

Last change on this file was 19532, checked in by westram, 7 months ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug 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
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 2.0 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      pt_server.hlp
5
6#       sub topics:
7#SUB     subtopic.hlp
8
9# format described in ../help.readme
10
11
12TITLE           PT_SERVER Administration
13
14OCCURRENCE      ARB_NT/Probes/PT_SERVER Admin
15
16DESCRIPTION     Allows you to start/kill and build/update 'PT_SERVER'
17                databases.
18
19                Select a 'PT_SERVER' and database from the menu displayed after
20                pressing the button below the 'PT_SERVER' prompt.
21
22                Start or kill the selected 'PT_SERVER' by pressing the
23                corresponding buttons.
24
25                Press the 'BUILD SERVER' button to export the current database
26                to the selected 'PT_SERVER' database.
27
28SECTION         PTSERVER for genes
29
30                In Genome Databases you may check the 'Gene server'-toggle to
31                build a PT-Server which is based on the sequences of the single
32                genes (and intergene regions) of all organisms.
33
34                Such a PT-Server allows to perform similarity searches and probe
35                design/match for single genes (in opposite to whole genomes with
36                a "normal" PT-Server).
37
38                When designing probes with such a gene PT-Server you always have
39                to validate these probes against a PT-Server build upon complete
40                genome sequences, otherwise you will get incorrect results for all
41                probes matching at beginning/end of a gene.
42
43
44NOTES           Read PT_SERVER: What Why and How if you do not understand this
45                helptext.
46
47                The probe designing and matching tools ('ARB_PROBE') and the
48                aligner of the editor ('ARB_EDIT4') rely on 'PT_SERVER'
49                databases and servers.
50
51                Update (re-build) the 'PT_SERVER' database when new
52                sequence (species) entries or sequence modifications (base
53                changes) have been introduced into the current database.
54
55                You can watch the progress of updating the PT_SERVER using
56                'View server log' (see also LINK{console.hlp}).
57
58EXAMPLES        None
59
60WARNINGS        None
61
62BUGS            No bugs known
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