source: branches/profile/HELP_SOURCE/oldhelp/faligner.hlp

Last change on this file was 8696, checked in by westram, 13 years ago
  • merge from saiali log:branches/saiali@8635-8695
    • unalign center (blockop)
    • modify SAI range (using ACI/SRT)
    • align ranges defined by SAI
    • refactorings
      • block ops
      • selection lists
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 5.1 KB
Line 
1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4UP      arb_edit4.hlp
5
6#Please insert subtopic references  (line starts with keyword SUB)
7#SUB    subtopic.hlp
8
9# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
10
11#************* Title of helpfile !! and start of real helpfile ********
12TITLE           The integrated aligners
13
14OCCURRENCE      ARB_EDIT4/Edit/Integrated Aligners
15
16DESCRIPTION     Currently there are two integrated aligners:
17
18                          1. Fast Aligner
19
20                          2. Island Hopper (see Subtopic)
21
22                The following adjustments and features should apply to both aligners.
23
24                We did not test everything yet with island hopper, so some of them are broken.
25                Please mail to LINK{devel@arb-home.de} if you find something.
26
27
28SECTION         ADJUSTMENTS
29
30                Align
31
32                                Align current, marked or selected sequences.
33
34                                If you type 'Ctrl-A' in the main editor window
35                                this option is set to align the current species and
36                                the aligner gets called.
37
38                Reference
39
40                                The aligner needs a sequence as reference.
41                                You can either select a fixed species, the
42                                consensus of the group containing the species
43                                or the next relative(s) found by the selected
44                                PT-Server.
45
46                                If you choose 'Auto search by pt_server', the
47                                aligner will use the next relative(s) as reference.
48                                If the nearest relative has gaps where the sequence
49                                to align has bases, the aligner will use the 2nd nearest
50                                relative or if that one has gaps too, the 3rd nearest, etc.
51                                You can define the maximum number of relatives.
52
53                                All used relatives and the number of base positions used from each relative,
54                                will be written into the field 'used_rels'.
55
56                                If you enter '0' in 'Data from range only, plus', relative
57                                search only uses data from the aligned range. If you enter
58                                a value different from '0' the used range will be
59                                expanded (positive values) or limited (negative values).
60                                When the input field is empty, the complete sequence will be used.
61
62                                Press 'More settings' to define how relative search works
63                                in detail. See LINK{next_neighbours_common.hlp}
64
65                Range
66
67                                Align only a part of or the whole sequence.
68
69                                Several possibilities exist for aligning just a part of the sequence:
70                                - select 'Positions around cursor' and specify how many positions shall be
71                                  taken into each direction from the cursor position (Example: If you align
72                                  10 columns around position 100 then columns 90-110 will be aligned).
73                                - if you use 'Selected range' the column range of the selected block will
74                                  be used.
75                                - if you select 'Multi-Range by SAI', the specified SAI will be interpreted as
76                                  a list of ranges. A list of characters defines what is considered a range.
77                                  All ranges will be aligned.
78
79                                See also LINK{e4_modsai.hlp} for howto create suitable SAIs.
80
81                Turn check
82
83                                The aligner is able to detect sequences which
84                                were entered in the wrong direction. With this
85                                switch you can select, if you like the aligner
86                                to turn such sequences and if it should ask you.
87
88                                NOTE: In two cases turn checking isn't
89                                reasonable:
90
91                                If you align only a part of a sequence or if you
92                                do not search Reference via pt_server. In both
93                                cases turn checking will be disabled.
94
95                Report
96
97                                The aligner can generate reports for the aligned
98                                sequence and for the reference sequence. These
99                                reports can be viewed with EDIT4, if you choose
100                                File/Load Configuration/DEFAULT_CONFIGURATION
101
102                                The report for the reference sequence (AMI)
103                                contains a '>' for every position were the aligner
104                                needed an insert in the reference sequence.
105
106                                The report for the aligned sequence (ASC) contains
107                                the following characters:
108
109                                    '-' for matching positions
110
111                                    '+' for inserts (in aligned sequence and in reference sequence)
112
113                                    '~' for matching, but not equal bases (A aligned to G, C aligned to T or U)
114
115                                    '#' for mismatching positions
116
117NOTES           This aligner knows about and uses all extended base characters
118                (ACGTUMRWSYKVHDN) for the alignment.
119                In other words: M aligned to R costs no penalty.
120
121EXAMPLES        None
122
123WARNINGS        None
124
125BUGS            If you select the menu entry 'remove all aligner entries' ARB_EDIT4
126                crashes in most cases.
127
128                Workaround:
129
130                        1. Close all groups containing species with aligner entries, so that no aligner entries are visible.
131                        2. Remove all aligner entries
132                        3. Reload configuration
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