The integrated alignersOCCURRENCE
ARB_NT/ARB_EDIT/EDIT/Integrated Aligners
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DESCRIPTION
Choose the 'Integrated aligners' item from the 'ARB_EDIT/Edit'
menu to display the 'Integrated aligners' window.
Currently there are two integrated aligners:
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Fast Aligner
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Island Hopper (see Subtopic)
The following adjustments and features should apply to both aligners.
We did not test everything yet with island hopper, so some of them are broken.
Please mail to devel@arb-home.de if you find something.
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ADJUSTMENTS
Align
Align selected or all marked sequences.
If you type 'Ctrl-A' in the main editor window
this option is set to selected species.
Reference
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The aligner needs a sequence as reference.
You can either select a fixed species, the
consensus of the group containing the species
or the next relative found by the selected
PT-Server.
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If you choose 'Auto search by pt_server', the
aligner will use the next relative to align.
If the nearest relative has gaps where the sequence
to align has bases, the aligner will use the 2nd nearest
relative or if that one has gaps too, the 3rd nearest, etc.
You can define the maximum number of relatives.
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All used relatives and the number of base positions used from each relative,
will be written into the field 'used_rels'.
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Press 'Settings' to define how relative search works
in detail. See ´Nearest relative search´
Range
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Align only a part or whole sequence.
If you align only a part of the sequence, then
you have to enter the number of columns around
the cursor.
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Example: If you align 10 columns around
position 100 then columns 90-110 get aligned.
Turn check
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The aligner is able to detect sequences which
were entered in the wrong direction. With this
switch you can select, if you like the aligner
to turn such sequences and if it should ask you.
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NOTE: In two cases turn checking isn't
reasonable:
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If you align only a part of a sequence or if you
do not search Reference via pt_server. In both
cases turn checking will be disabled.
Report
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The aligner can generate reports for the aligned
sequence and for the reference sequence. These
reports can be viewed with EDIT4, if you choose
File/Load Configuration/DEFAULT_CONFIGURATION
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The report for the reference sequence (AMI)
contains a '>' for every position were the aligner
needed an insert in the reference sequence.
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The report for the aligned sequence (ASC) contains
the following characters:
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'-' for matching positions
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'+' for inserts (in aligned sequence and in reference sequence)
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'~' for matching, but not equal bases (A aligned to G, C aligned to T or U)
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'#' for mismatching positions
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NOTES
This aligner knows about and uses all extended base characters
(ACGTUMRWSYKVHDN) for the alignment.
In other words: M aligned to R costs no penalty.
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EXAMPLESWARNINGSBUGS
If you select the menu entry 'remove all aligner entries' ARB_EDIT4
crashes in most cases.
Workaround:
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Close all groups containing species with aligner entries, so that no aligner entries are visible.
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Remove all aligner entries
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Reload configuration
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