| 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 security.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 insdel.hlp |
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| 8 | |
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| 9 | |
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| 10 | #************* Title of helpfile !! and start of real helpfile ******** |
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| 11 | |
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| 12 | |
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| 13 | TITLE Alignment Administration |
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| 14 | |
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| 15 | OCCURRENCE ARB_NT/Sequence/Admin |
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| 16 | ARB_MERGE/Check alignments/MODIFY |
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| 17 | |
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| 18 | DESCRIPTION This module allows handling and modification of 'alignments' |
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| 19 | (see LINK{glossary.hlp}). |
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| 20 | |
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| 21 | Select an alignment from the 'Alignments' subwindow |
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| 22 | |
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| 23 | Define the type of sequences (DNA, RNA, protein): |
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| 24 | |
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| 25 | Press the <Type of Sequences> button and choose from the |
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| 26 | displayed menu. |
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| 27 | |
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| 28 | Set protection: |
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| 29 | |
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| 30 | Press the <Default Write Protection> button and choose |
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| 31 | from the displayed menu. |
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| 32 | |
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| 33 | Press the respective buttons to perform further functions: |
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| 34 | |
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| 35 | DELETE: Delete an alignment and its sequence data |
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| 36 | RENAME: Rename an alignment |
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| 37 | CREATE: Create a new alignment (no data) |
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| 38 | COPY: Copy an alignment |
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| 39 | CHECK LEN: Find the longest sequence and set the |
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| 40 | 'Maximum Seq. Length' displayed in the |
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| 41 | corresponding subwindow |
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| 42 | FORMAT: Append '.' to sequences up to 'Maximum Seq. |
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| 43 | Length'. |
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| 44 | |
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| 45 | Auto format: Whether to ask, format or skip w/o asking |
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| 46 | whenever an unformatted alignment is detected. |
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| 47 | |
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| 48 | NOTES Some functions require setting a protection level equal to or |
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| 49 | higher than that of the 'alignment'. |
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| 50 | |
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| 51 | There is one special alignment called "ali_genom" used for full |
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| 52 | genome sequences. You can't format that alignment because it is |
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| 53 | necessary to ensure that it's alignment positions match those |
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| 54 | used in the gene entries. For the same reason you should never |
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| 55 | ever put any gap into that alignment. |
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| 56 | |
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| 57 | EXAMPLES None |
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| 58 | |
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| 59 | WARNINGS Be careful when deleting or changing the name of an alignment |
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| 60 | while other programs are using it (eg. parsimony programs ..) |
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| 61 | |
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| 62 | BUGS No bugs known |
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