| 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 Maximum base frequency |
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| 12 | |
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| 13 | Calculate the Percentage of the Most Frequent Base |
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| 14 | |
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| 15 | OCCURRENCE ARB_NT/SAI/create SAI/Max Frequency |
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| 16 | |
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| 17 | DESCRIPTION Finds the most frequent base (or gap) in each column for all marked |
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| 18 | species. Then the number of all sequences with this base are |
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| 19 | divided by: |
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| 20 | |
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| 21 | * the number of all marked sequences (if not ignoring gaps) |
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| 22 | * the number of bases in this column (if ignoring gaps) |
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| 23 | |
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| 24 | The resulting percentage is divided by ten and then the second last |
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| 25 | digit is taken: |
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| 26 | |
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| 27 | 0% - 19% -> '1' (does not occur for nucleotides) |
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| 28 | 20% - 29% -> '2' |
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| 29 | 30% - 39% -> '3' |
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| 30 | ... |
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| 31 | 90% - 99% -> '9' |
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| 32 | 100% -> '0' |
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| 33 | |
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| 34 | |
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| 35 | NOTE The result can be used as a conservation profile and filter. |
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| 36 | Rule of thumb: |
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| 37 | the higher the number, the more conserved the position (but mind the '0' which means 100%!). |
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| 38 | |
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| 39 | Internally the SAI consists of two lines: the main line called 'data' and a second line called 'dat2'. |
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| 40 | |
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| 41 | The first is used when you use the SAI as conservation profile or filter and |
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| 42 | contains the SECOND LAST digit of the calculated frequencies. |
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| 43 | |
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| 44 | The second contains the LAST digit of the calculated frequencies. It is not used and does only |
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| 45 | show up, when you load the SAI into ARB_EDIT4, where it will show both lines. |
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| 46 | |
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| 47 | EXAMPLES Say one column contains 7 A's 4 G's and 5 Gaps. |
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| 48 | |
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| 49 | * ignoring gaps will result in 7/11 == 64 % which is converted to '6'. |
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| 50 | * otherwise we get 7/16 == 44% which will be indicated by a '4' in the target sequence. |
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| 51 | |
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| 52 | SECTION Gaps |
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| 53 | |
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| 54 | If gaps are ignored '-' are treated like '.': both get removed and frequency is calculated on non-gaps only. |
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| 55 | |
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| 56 | If gaps are NOT ignored, '-' are treated like non-gaps, i.e. a column containing only '-' will be assigned a |
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| 57 | max. frequency of 100%. '.' are treated as gaps. |
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| 58 | |
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| 59 | SECTION Ambiguities |
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| 60 | |
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| 61 | Ambiguities are counted proportionally, i.e. |
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| 62 | |
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| 63 | * a 'N' counts as 1/4 'A', 1/4 'C', 1/4 'G' and 1/4 'T' |
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| 64 | * a 'D' counts as 1/3 'A', 1/3 'G' and 1/3 'T' |
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| 65 | * a 'Y' counts as 1/2 'C' and 1/2 'T' |
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| 66 | |
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| 67 | Example: |
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| 68 | |
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| 69 | A column containing 9 'C' and one 'Y' results in a max. frequency of 95% (=9.5 'C'). |
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| 70 | |
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| 71 | BUGS No bugs known yet |
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