| 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 | #Please insert subtopic references (line starts with keyword SUB) |
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| 5 | |
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| 6 | SUB extended.hlp |
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| 7 | SUB security.hlp |
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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 ******** |
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| 11 | TITLE SAI Administration |
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| 12 | |
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| 13 | OCCURRENCE ARB_NT/SAI/Manage SAIs |
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| 14 | |
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| 15 | DESCRIPTION This tool allows to delete, rename, copy and edit 'SAI' entries. |
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| 16 | SAI is short for "sequence associated information". |
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| 17 | |
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| 18 | The database entries contained in the selected SAI are displayed in the |
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| 19 | 'Info Box' subwindow. |
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| 20 | |
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| 21 | Howto generate SAIs: |
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| 22 | |
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| 23 | Most SAIs will be generated by functions from the SAI menu in the ARB main window. |
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| 24 | |
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| 25 | It is as well possible to convert a species into an SAI (see LINK{sp_sp_2_ext.hlp}). |
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| 26 | SAIs can be converted into species entries by pressing the <COPY TO SPECIES> button. |
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| 27 | |
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| 28 | It is also possible to calculate SAI (from other SAI) using the LINK{saicalc.hlp}. |
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| 29 | |
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| 30 | SAI grouping: |
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| 31 | |
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| 32 | Each SAI belongs to a group of SAIs. These groups appear in ARB_EDIT4. |
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| 33 | Use the 'ASSIGN GROUP' button to define the group membership of the |
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| 34 | select SAI. |
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| 35 | |
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| 36 | SAI editing: |
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| 37 | |
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| 38 | Editing SAI data is possible using the sequence editor (see LINK{e4.hlp}). |
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| 39 | |
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| 40 | SAI may have alignment specific comments in each ali_xxx-CONTAINER. |
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| 41 | These comments are stored in the "_TYPE" field. |
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| 42 | The "EDIT COMMENT" button will always edit the comment associated with the |
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| 43 | alignment currently selected in the arb main window. |
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| 44 | |
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| 45 | Using the "Edit at top" entry, you may define, which SAI |
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| 46 | show up in the top area of the sequence editor by default. |
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| 47 | |
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| 48 | NOTES It may be necessary to set the protection level equal or higher |
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| 49 | than that assigned to the particular 'SAI' entry. |
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| 50 | |
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| 51 | An example macro ("keep_listed_SAIs.amc") is delivered together with ARB, |
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| 52 | which allows to delete all unwanted SAIs from a database, by defining |
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| 53 | a list of all SAIs to keep. |
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| 54 | That macro can be found using the file-prompter |
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| 55 | under LINK{macro.hlp} (see EXAMPLES section there). |
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| 56 | |
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| 57 | EXAMPLES None |
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| 58 | |
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| 59 | WARNINGS None |
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| 60 | |
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| 61 | BUGS No bugs known |
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