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Last update on 04. Dec 2013 .
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The integrated aligners

OCCURRENCE

ARB_NT/ARB_EDIT/EDIT/Integrated Aligners

 

DESCRIPTION

Choose the 'Integrated aligners' item from the 'ARB_EDIT/Edit' menu to display the 'Integrated aligners' window.

Currently there are two integrated aligners:

  1. Fast Aligner
  2. 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.

 

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

  • 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.
  • 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.
  • All used relatives and the number of base positions used from each relative, will be written into the field 'used_rels'.
  • Press 'Settings' to define how relative search works in detail. See ´Nearest relative search´

Range

  • 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.
  • Example: If you align 10 columns around position 100 then columns 90-110 get aligned.

Turn check

  • 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.
  • NOTE: In two cases turn checking isn't reasonable:
  • 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

  • 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
  • The report for the reference sequence (AMI) contains a '>' for every position were the aligner needed an insert in the reference sequence.
  • The report for the aligned sequence (ASC) contains the following characters:
    • '-' for matching positions
    • '+' for inserts (in aligned sequence and in reference sequence)
    • '~' for matching, but not equal bases (A aligned to G, C aligned to T or U)
    • '#' for mismatching positions


 

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.

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

If you select the menu entry 'remove all aligner entries' ARB_EDIT4 crashes in most cases.

Workaround:

  1. Close all groups containing species with aligner entries, so that no aligner entries are visible.
  2. Remove all aligner entries
  3. Reload configuration