| 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 pt_server.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 subtopic.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 PT_SERVER Administration |
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| 13 | |
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| 14 | OCCURRENCE ARB_NT/Probes/PT_SERVER Admin |
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| 15 | |
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| 16 | DESCRIPTION Allows you to start/kill and build/update 'PT_SERVER' |
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| 17 | databases. |
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| 18 | |
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| 19 | Select a 'PT_SERVER' and database from the menu displayed after |
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| 20 | pressing the button below the 'PT_SERVER' prompt. |
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| 21 | |
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| 22 | Start or kill the selected 'PT_SERVER' by pressing the |
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| 23 | corresponding buttons. |
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| 24 | |
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| 25 | Press the 'BUILD SERVER' button to export the current database |
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| 26 | to the selected 'PT_SERVER' database. |
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| 27 | |
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| 28 | SECTION PTSERVER for genes |
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| 29 | |
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| 30 | In Genome Databases you may check the 'Gene server'-toggle to |
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| 31 | build a PT-Server which is based on the sequences of the single |
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| 32 | genes (and intergene regions) of all organisms. |
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| 33 | |
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| 34 | Such a PT-Server allows to perform similarity searches and probe |
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| 35 | design/match for single genes (in opposite to whole genomes with |
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| 36 | a "normal" PT-Server). |
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| 37 | |
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| 38 | When designing probes with such a gene PT-Server you always have |
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| 39 | to validate these probes against a PT-Server build upon complete |
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| 40 | genome sequences, otherwise you will get incorrect results for all |
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| 41 | probes matching at beginning/end of a gene. |
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| 42 | |
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| 43 | |
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| 44 | NOTES Read PT_SERVER: What Why and How if you do not understand this |
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| 45 | helptext. |
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| 46 | |
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| 47 | The probe designing and matching tools ('ARB_PROBE') and the |
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| 48 | aligner of the editor ('ARB_EDIT4') rely on 'PT_SERVER' |
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| 49 | databases and servers. |
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| 50 | |
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| 51 | Update (re-build) the 'PT_SERVER' database when new |
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| 52 | sequence (species) entries or sequence modifications (base |
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| 53 | changes) have been introduced into the current database. |
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| 54 | |
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| 55 | You can watch the progress of updating the PT_SERVER using |
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| 56 | 'View server log' (see also LINK{console.hlp}). |
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| 57 | |
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| 58 | EXAMPLES None |
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| 59 | |
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| 60 | WARNINGS None |
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| 61 | |
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| 62 | BUGS No bugs known |
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