source: branches/port5/HELP_SOURCE/oldhelp/next_neighbours_common.hlp

Last change on this file was 6142, checked in by westram, 16 years ago
  • backport [6141] (parts not affecting code at all, i.e. helpfiles, figs, ..)
File size: 4.1 KB
Line 
1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4UP      pt_server.hlp
5
6#Please insert subtopic references  (line starts with keyword SUB)
7SUB     next_neighbours.hlp
8SUB     next_neighbours_listed.hlp
9SUB     faligner.hlp
10
11# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
12
13#************* Title of helpfile !! and start of real helpfile @@@ ********
14TITLE           Nearest relative search
15
16OCCURRENCE      ARB_NT/Search/More search/Search Next Relatives of SELECTED Species in PT Server
17                ARB_NT/Search/More search/Search Next Relatives of LISTED Species in PT Server
18                ARB_NT/ARB_EDIT/EDIT/Integrated Aligners
19
20SECTION         ALGORITHM
21
22                Splits the sequence(s) into short oligos of a given size.
23                These oligos are 'Probe Matched' against the PT_SERVER database.
24                The more hits within the sequence of another species, the more related the other species is.
25
26SECTION         PARAMETERS
27
28                PT-Server
29
30                        Select the PT-Server to search
31
32                Oligo length
33
34                        Length of oligos used to perform probe match against the PT server.
35                        Default is 12.
36
37                Mismatches
38
39                        Number of mismatches allowed per oligo.
40                        Default is 0.
41
42                        Be careful: The search may get incredible slow, when rising the number of mismatches.
43
44                Search mode
45
46                       Complete:        Match all possible oligos
47                       Quick:           Only match oligos starting with 'A'
48
49                       The 'Quick mode' works well for many sequence types and is approx. 4 times
50                       faster than the 'Complete mode'. For some sequence types it completely fails,
51                       e.g. if there are repetitive areas containing many 'AAAAA'
52
53                Match score:
54
55                       absolute:        returns the absolute number of hits
56                       relative:        returns the number of hits relative to maximum possible hits
57
58                       The score depends on several other parameters like number of allowed mismatches,
59                       search mode, oligo length and complement settings.
60
61                       The maximum absolute score is
62
63                           (length of relatives sequence) minus (oligo length)
64
65                       Practically this score is rarely reached, because several possible oligos are
66                       skipped, namely
67
68                                - all oligos starting with 2 identical nucleotides
69                                - all oligos containing IUPAC codes (or N's)
70
71                       If mismatches are used, each oligo may hit at several positions. Thus the
72                       maximum relative score may exceed 100% (and the maximum absolute score may
73                       exceed its theoretical maximum).
74
75                       If you use 'Quick mode' the mean relative score will be approx. 25% (assuming
76                       that 25% of the possible oligos start with an 'A').
77
78                       That means.. only if you use
79
80                            - 0 mismatches,
81                            - 'Complete mode' and
82                            - your sequences contain no IUPACs and no repetitions,
83
84                       you will get a score of 100% (or sequenceLength-oligoLength) for
85                       the selected species itself and its duplicates.
86
87                Complement:
88
89                       forward:             Match only forward oligos
90                       reverse:             Match only reverse oligos
91                       complement:          Match only complement oligos
92                       reverse-complement:  Match only reverse-complement oligos
93                       and all combinations of these.
94
95                       The combinations may affect the score as well!
96
97                       Note: Not available for EDIT4 aligner.
98
99NOTES           None
100
101EXAMPLES        None
102
103WARNINGS        None
104
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