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

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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)
7SUB     islandhopping.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
42
43                                    * select a fixed species by name,
44                                    * the consensus of the group containing the aligned species or
45                                    * the next relative(s) found by the selected PT-Server.
46
47                                If you choose 'Species by name', you may press the 'COPY' button
48                                to copy the name of the 'Current Species' to the 'Reference' species.
49                                Alternatively you may use CTRL-R while the focus is inside the sequence view
50                                (Note: CTRL-R does not work, if LINK{viewdiff.hlp} is active).
51
52                                If you choose 'Auto search by pt_server', the
53                                aligner will use the next relative(s) as reference.
54
55                                 * Please read section about 'Protein alignment with pt_server' below.
56
57                                 * If the nearest relative has gaps where the sequence
58                                   to align has bases, the aligner will use the 2nd nearest
59                                   relative or if that one has gaps too, the 3rd nearest, etc.
60                                   You can define the maximum number of relatives considered.
61
62                                 * All used relatives and the number of base positions used from each relative,
63                                   will be written into the field 'used_rels' (see also LINK{markbyref.hlp}).
64
65                                If you enter '0' in 'Data from range only, plus', relative
66                                search only uses data from the aligned range. If you enter
67                                a value different from '0' the used range will be
68                                expanded (positive values) or limited (negative values).
69                                When the input field is empty, the complete sequence will be used.
70
71                                Press 'More settings' to define how relative search works
72                                in detail. See LINK{next_neighbours_common.hlp}
73
74                Range
75
76                                Align only a part of or the whole sequence.
77
78                                Several possibilities exist for aligning just a part of the sequence:
79                                - select 'Positions around cursor' and specify how many positions shall be
80                                  taken into each direction from the cursor position (Example: If you align
81                                  10 columns around position 100 then columns 90-110 will be aligned).
82                                - if you use 'Selected range' the column range of the selected block will
83                                  be used.
84                                - if you select 'Multi-Range by SAI', the specified SAI will be interpreted as
85                                  a list of ranges. A list of characters defines what is considered a range.
86                                  All ranges will be aligned.
87
88                                See also LINK{e4_modsai.hlp} for howto create suitable SAIs.
89
90                Turn check
91
92                                The aligner is able to detect sequences which
93                                were entered in the wrong direction. With this
94                                switch you can select, if you like the aligner
95                                to turn such sequences and if it should ask you.
96
97                                NOTE: In two cases turn checking isn't
98                                reasonable:
99
100                                If you align only a part of a sequence or if you
101                                do not search Reference via pt_server. In both
102                                cases turn checking will be disabled.
103
104                Report
105
106                                The aligner can generate reports for the aligned
107                                sequence and for the reference sequence. These
108                                reports can be viewed with EDIT4, if you choose
109                                File/Load Configuration/DEFAULT_CONFIGURATION
110
111                                The report for the reference sequence (AMI)
112                                contains a '>' for every position were the aligner
113                                needed an insert in the reference sequence.
114
115                                The report for the aligned sequence (ASC) contains
116                                the following characters:
117
118                                    '-' for matching positions
119
120                                    '+' for inserts (in aligned sequence and in reference sequence)
121
122                                    '~' for matching, but not equal bases (A aligned to G, C aligned to T or U)
123
124                                    '#' for mismatching positions
125
126SECTION         Protein alignment with pt_server
127
128                If you want to align protein sequences and use a PT-Server (to detect
129                the next relative for each sequence),
130                you need to
131
132                     * have two alignments in your database (a protein alignment and a
133                       corresponding DNA alignment). ARB has functions to synchronize these
134                       alignments (see LINK{aaali.hlp}),
135                     * build a pt_server based on the DNA-alignment,
136                       select that pt_server in the aligner window and
137                     * specify the name of the DNA-alignment in the 'Alignment' field.
138
139NOTES           This aligner knows about and uses all extended base characters
140                (ACGTUMRWSYKVHDN) for the alignment.
141                In other words: M aligned to R costs no penalty.
142
143                The config-manager icon handles the settings in the 'Integrated Aligners' window and those in
144                its subwindows 'Parameters for Island Hopping' and 'Family search parameters'.
145
146EXAMPLES        None
147
148WARNINGS        None
149
150BUGS            If you select the menu entry 'remove all aligner entries' ARB_EDIT4
151                crashes in most cases.
152
153                Workaround:
154
155                        1. Close all groups containing species with aligner entries, so that no aligner entries are visible.
156                        2. Remove all aligner entries
157                        3. Reload configuration
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