| 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 | |
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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 | |
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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 Join species |
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| 12 | |
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| 13 | OCCURRENCE ARB_NT/Species/Merge Species/Join marked species |
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| 14 | |
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| 15 | DESCRIPTION |
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| 16 | |
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| 17 | WARNING: This module is obsolete by newer modules. See NOTES below! |
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| 18 | |
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| 19 | "Join species" merges several similar species into one species. |
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| 20 | |
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| 21 | All database fields and the sequences get concatenated. |
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| 22 | |
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| 23 | - Mark all species that should be examined for similarity. |
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| 24 | |
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| 25 | - Select a database field entry from the list |
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| 26 | to set a similarity-criterion used to detect |
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| 27 | candidates for joining (for e.g., full_name). |
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| 28 | |
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| 29 | - Check separators for fields and sequences. |
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| 30 | |
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| 31 | - Press GO to start. |
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| 32 | |
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| 33 | EXAMPLES |
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| 34 | |
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| 35 | For example you have a 23s and a 16s database and you want |
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| 36 | to append the 16s to the 23s sequences than you have to do: |
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| 37 | |
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| 38 | - merge the 16s to the 23s sequences. |
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| 39 | |
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| 40 | - create a field 'species_name' which holds the |
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| 41 | real name of the species. |
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| 42 | That means the species_name of the 16s sequence |
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| 43 | should be the same as of the 23s seq. |
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| 44 | Do not use the 'name'-field because it is |
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| 45 | used as a UNIQUE id to the database. |
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| 46 | |
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| 47 | - ARB_NT/Species/Merge Species/Join Marked Species |
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| 48 | and use the field 'species_name'. |
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| 49 | |
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| 50 | |
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| 51 | NOTES There's a second, newer function to merge species: see LINK{merge_species.hlp} |
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| 52 | |
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| 53 | There's a special new function to concatenate alignments: see LINK{concatenate.hlp} |
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| 54 | |
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| 55 | WARNINGS 'Join marked species' does only merge fields of type STRING, all other fields are skipped |
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| 56 | (taken from one of the joined species). |
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| 57 | |
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| 58 | BUGS No bugs known |
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