| 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 species_join.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 Merge Similar Species |
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| 12 | |
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| 13 | OCCURRENCE ARB_NT/Species/Merge Species/Create merged species from similar species |
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| 14 | ARB_NT/Sequence/Concatenate sequences/MERGE SIMILAR SPECIES |
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| 15 | |
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| 16 | DESCRIPTION |
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| 17 | |
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| 18 | "Merge Similar Species" creates new species by merging |
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| 19 | fields and alignments of several similar species. |
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| 20 | |
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| 21 | - Mark all species that should be examined for similarity. |
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| 22 | |
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| 23 | - Select a database field entry by clicking on the first |
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| 24 | button to set a similarity-criterion used to detect |
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| 25 | candidates for merging (for e.g., full_name). |
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| 26 | |
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| 27 | - Specify the new field name to which the "number of merged |
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| 28 | species" information is to be stored (e.g., merged_species). |
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| 29 | |
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| 30 | - Press "Merge similar species ..." to start. |
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| 31 | |
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| 32 | SECTION Merge and concatenate |
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| 33 | |
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| 34 | From LINK{concatenate.hlp} you can access a special flavor of the |
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| 35 | "Merge similar species" function, that will also concatenate the |
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| 36 | selected alignments. |
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| 37 | |
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| 38 | That version is useful after merging species of two (or more) independent |
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| 39 | databases, that contain different genes of the same organisms. |
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| 40 | |
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| 41 | After merging you'll end up with data like: |
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| 42 | |
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| 43 | name "SpecExe1" |
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| 44 | full_name "Species exemplares" |
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| 45 | ali_5s/data "--AC--GU--" |
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| 46 | |
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| 47 | name "SpecAlt1" |
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| 48 | full_name "Species alternatio" |
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| 49 | ali_5s/data "--AU-GGC--" |
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| 50 | |
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| 51 | name "SpecExe2" |
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| 52 | full_name "Species exemplares" |
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| 53 | ali_16s/data "----U-A---G-C-----" |
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| 54 | |
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| 55 | name "SpecAlt2" |
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| 56 | full_name "Species alternatio" |
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| 57 | ali_16s/data "----G-A---UUC-----" |
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| 58 | |
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| 59 | |
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| 60 | Using merge and concatenate with 'full_name' as similarity criterion, |
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| 61 | you can generate data like |
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| 62 | |
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| 63 | name "SpecExe3" |
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| 64 | full_name "Species exemplares" |
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| 65 | ali_5s_and_16s/data "--AC--GU--XXX----U-A---G-C-----" |
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| 66 | |
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| 67 | name "SpecAlt3" |
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| 68 | full_name "Species alternatio" |
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| 69 | ali_5s_and_16s/data "--AU-GGC--XXX----G-A---UUC-----" |
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| 70 | |
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| 71 | |
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| 72 | NOTES There's a second (older) function to merge species: see LINK{species_join.hlp} |
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| 73 | |
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| 74 | EXAMPLES None |
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| 75 | |
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| 76 | WARNINGS None |
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| 77 | |
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| 78 | BUGS No bugs known |
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