source: branches/lib/HELP_SOURCE/source/max_freq.hlp

Last change on this file was 19532, checked in by westram, 4 months ago
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6#SUB     subtopic.hlp
7
8# format described in ../help.readme
9
10
11TITLE           Maximum base frequency
12
13                Calculate the Percentage of the Most Frequent Base
14
15OCCURRENCE      ARB_NT/SAI/create SAI/Max Frequency
16
17DESCRIPTION     Finds the most frequent base (or gap) in each column for all marked
18                species. Then the number of all sequences with this base are
19                divided by:
20
21                        * the number of all marked sequences (if not ignoring gaps)
22                        * the number of bases in this column (if ignoring gaps)
23
24                The resulting percentage is divided by ten and then the second last
25                digit is taken:
26
27                        0%  - 19%  ->  '1' (does not occur for nucleotides)
28                        20% - 29%  ->  '2'
29                        30% - 39%  ->  '3'
30                        ...
31                        90% - 99%  ->  '9'
32                        100%       ->  '0'
33
34
35NOTE            The result can be used as a conservation profile and filter.
36                Rule of thumb:
37                the higher the number, the more conserved the position (but mind the '0' which means 100%!).
38
39                Internally the SAI consists of two lines: the main line called 'data' and a second line called 'dat2'.
40
41                  The first is used when you use the SAI as conservation profile or filter and
42                  contains the SECOND LAST digit of the calculated frequencies.
43
44                  The second contains the LAST digit of the calculated frequencies. It is not used and does only
45                  show up, when you load the SAI into ARB_EDIT4, where it will show both lines.
46
47EXAMPLES        Say one column contains 7 A's 4 G's and 5 Gaps.
48
49                 * ignoring gaps will result in 7/11 == 64 % which is converted to '6'.
50                 * otherwise we get 7/16 == 44% which will be indicated by a '4' in the target sequence.
51
52SECTION         Gaps
53
54                If gaps are ignored '-' are treated like '.': both get removed and frequency is calculated on non-gaps only.
55
56                If gaps are NOT ignored, '-' are treated like non-gaps, i.e. a column containing only '-' will be assigned a
57                max. frequency of 100%. '.' are treated as gaps.
58
59SECTION         Ambiguities
60
61                Ambiguities are counted proportionally, i.e.
62
63                  * a 'N' counts as 1/4 'A', 1/4 'C', 1/4 'G' and 1/4 'T'
64                  * a 'D' counts as 1/3 'A', 1/3 'G' and 1/3 'T'
65                  * a 'Y' counts as 1/2 'C' and 1/2 'T'
66
67                Example:
68
69                        A column containing 9 'C' and one 'Y' results in a max. frequency of 95% (=9.5 'C').
70
71BUGS            No bugs known yet
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