| 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 arb_edit.hlp |
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| 5 | #Please insert subtopic references (line starts with keyword SUB) |
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| 6 | #SUB subtopic.hlp |
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| 7 | SUB pt_server.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 Align Sequence |
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| 13 | |
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| 14 | OCCURRENCE ARB_NT/ARB_EDIT/EDIT/Align Sequence |
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| 15 | |
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| 16 | DESCRIPTION Aligns or realigns selected sequence with the database |
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| 17 | sequences. The most similar database sequences are |
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| 18 | found, and the new sequence is aligned with these according to |
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| 19 | primary and secondary structure similarity. |
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| 20 | |
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| 21 | Choose the 'Align Sequence' item from the 'ARB_EDIT/EDIT' menu |
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| 22 | to display the 'ALIGNER' window. |
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| 23 | |
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| 24 | Select a sequence by positioning the cursor on the name and |
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| 25 | double clicking the left mouse button. |
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| 26 | |
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| 27 | Choose the appropriate 'PT_SERVER' database from the menu |
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| 28 | displayed after pressing the <Search relatives in> |
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| 29 | button. (For example, to align a 16S-like rRNA select |
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| 30 | 16s_rrna_aligned.arb.) |
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| 31 | |
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| 32 | Define whether the most closely related species of the database |
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| 33 | should be marked or not by pressing the <Mark used |
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| 34 | relatives> button. |
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| 35 | |
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| 36 | Press the <ALIGN> button. |
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| 37 | |
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| 38 | NOTES The search for the most similar sequences is performed by the |
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| 39 | 'PT-server'. This server needs a special external database for |
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| 40 | rapid search. This database is not synchronized with the current |
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| 41 | database and has to be updated from time to time by a computing-time expensive procedure ('ARB_NT/ETC/Probe Admin'). |
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| 42 | |
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| 43 | Marking the closest relatives allows manual optimization of the alignment of the new species with its closest relatives. |
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| 44 | |
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| 45 | EXAMPLES None |
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| 46 | |
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| 47 | WARNINGS The aligner version available with the present package often |
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| 48 | does not properly align short partial sequences. |
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| 49 | |
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| 50 | BUGS The aligner needs lots of computer memory, sometimes more than |
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| 51 | you have. In this case it may not align some sequences. |
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| 52 | |
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| 53 | The aligner does not align the last 3-6 bases of short sequences |
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| 54 | correctly. Look at the end of your sequences. |
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