source: branches/tree/HELP_SOURCE/source/sina_main.hlp

Last change on this file was 18769, checked in by westram, 4 years ago
  • move all helpfiles to new source location
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1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
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5#Please insert subtopic references  (line starts with keyword SUB)
6#SUB    subtopic.hlp
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8# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
9
10#************* Title of helpfile !! and start of real helpfile ********
11TITLE           Graph Aligner
12
13OCCURRENCE      ARB Editor -> Edit -> Prototypical Graph Aligner
14
15DESCRIPTION     This is an alternative to the integrated aligners developed for the SILVA
16                project. Similar to those aligners it uses aligned sequences from your
17                current database as a reference to align the selected sequences. Other than
18                them it employs full dynamic programming to create the alignment. It also
19                considers all selected relatives at once, instead of falling back to less
20                similar sequences only if the current sequence is missing bases (e.g.
21                because it is a partial sequence).
22
23SECTION         OPTIONS
24
25                Select the sequences to be aligned as usual ("Current Species", "Selected
26                Species", "Marked Species").
27
28
29                Select a PT-Server to be used. Make sure it is up to date and contains all
30                sequences you want to be considered as reference.
31
32                HINT: Unless you deselect the "Realign" button in the advanced menu, no
33                sequence will be used as a reference for itself.
34
35                HINT: Sequences with less than 10 gaps are considered not aligned, and
36                also not used as a reference.
37
38
39                Select a positional variability filter. If possible, use the filter
40                appropriate for the type of sequences you want aligned. Positional
41                variability statistics will be considered when placing the individual bases.
42
43
44                Decide what to do with possible overhang. If your sequence extends beyond the
45                reference sequences on either side of the alignment, those bases cannot be
46                aligned properly. Three options of handling this situation are supported:
47
48                "keep attached"
49
50                        just leave them dangling, directly attached to the last base that
51                        could be aligned properly
52
53                "move to edge"
54
55                        move them out to the very beginning and end of
56                        the alignment. This allows you to easily spot sequences
57                        with overhang, and decide what to do yourself. Recommended,
58                        but only if you check your sequences after alignment!
59
60                "remove"
61
62                        automatically remove these bases.
63
64
65                Select a protection level higher than that of the sequences if you want the
66                alignment software to actually modify the bases. Choose a lower protection
67                level to execute a "dry run", not changing anything. Note that sequences
68                with a protection level of zero will always be changed.
69
70
71                The Logging Level option allows you to change the noisiness of the alignment
72                program. All output will be printed to the console from which you started
73                ARB. The Option "debug_graph" may produce several large files for every
74                sequence aligned and is not recommended for the uninitiated.
75
76SECTION         TRICKS
77
78                If you want to see how the alignment that would be produced by the graph
79                aligner differs from your current alignment, and why the program would
80                act that way, you can set the protection level to "0" and the Logging level
81                to "debug". The output on the console will now include all differing sections
82                of the alignment and the matching parts of the reference sequences.
83
84SECTION         ADVANCED OPTIONS
85
86                Select the "Show advanced options" Button at the top to gain access to
87                the you-may-now-shoot-yourself-in-the-foot-severely dialog window.
88
89                Don't be surprised if the graph aligner crashes after you entered silly
90                values here. No sanity check of your options is done.
91
92
93                Turn check:
94
95                        If selected (default) sequences will be automatically reversed
96                        and/or complemented if this will likely improve the alignment.
97
98
99                Realign:
100
101                        If selected, the sequence itself is excluded from the result of
102                        the executed PT-Server family search. If deselected, the alignment
103                        of an identical sequence found by the PT-Server is copied.
104
105
106                Load reference sequence from PT Server:
107
108                        Do not read alignment data from your current database, but from the
109                        database the PT-Server was built from. This makes starting the
110                        graph aligner much slower, but allows you to align against external
111                        databases or PT-Servers with different sequence names than your
112                        current database.
113
114
115                (Copy and) mark sequence used as reference:
116
117                        Mark the sequences that were used as a reference during alignment.
118                        This allows you to easily load them into the editor to review the
119                        decisions made by the graph aligner.
120                        If you also selected the "Load reference" option, sequences will be
121                        copied into your current database prior to being marked.
122
123
124                Gap insertion/extension penalties: (default is 5/2)
125
126                        You can change the penalties associated with opening and extending
127                        gaps.
128
129
130                Family search min/min_score/max: (default 15,0.7,40)
131
132                        The first value tells the graph aligner how many sequences it should
133                        try to always use. The second value determines the minimal identity
134                        with the target sequence additional reference sequences should have.
135                        The third value selects the maximal number of sequences to be used
136                        as a reference.
137
138
139                Use at least X sequences with at least Y bases: (SSU-default is 1, 1400)
140
141                        This option allows you to require that the reference include X
142                        sequences of a length larger than or equal to Y.
143
144
145                Aligner threads / Queue size:
146
147                        Up to 4 threads can be used to align simultaneously. If your workstation
148                        sports multiple CPUs this will speed up alignment of many sequences.
149                        Increase the size of the buffer between the graph aligner components to
150                        about 15 when using 4 threads.
151
152
153WARNINGS        None
154
155BUGS            No bugs known
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