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Last update on 25. Nov 2018 .
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Realign DNA

OCCURRENCE

ARB_NT/Sequence/Align sequences/Realign DNA according to aligned protein

 

DESCRIPTION

If you have translated DNA sequences into protein sequences and then have aligned the resulting protein sequences, this function can be used to re-align the DNA sequences according to the (modified) protein alignment.

Select the protein and the corresponding DNA alignment.

Press 'REALIGN' to re-align the DNA sequences of all marked species.

 

Options

The length of the DNA alignment has to be at least 3 times the length of the protein alignment. If it is shorter, the realigner will automatically increase the length if 'Increase DNA alignment size if needed' is checked. Otherwise it will abort with error.

By checking 'Unmark successfully realigned species' you can control whether to leave all species marked or only species failing to realign, which might be helpful to examine and fix failure reasons.

If your DNA alignment has some extra DNA beyond one or both ends of the part coding the protein alignment, the ARB realigner will still be able to find and realign the coding part properly. The extra DNA can either

  • be appended adjacent to the coding part (if there is enough space) or
  • be cut off.

You can control that behavior by checking 'Cut-off superfluous DNA'.

 

Fields 'transl_table' and 'codon_start'

If the species contains a field 'transl_table' (which should contain the translation table number as used by the EMBL database) it is used to detect the correct translation table. If no such field is defined a translation-table-auto-detection takes place.

If the species contains a field 'codon_start' it is overwritten with '1' in order to make further translations of the realigned DNA work properly.

Either both fields ('transl_table' and 'codon_start') or none of them has to exist. Otherwise an error occurs and you have to correct these fields manually (e.g. by using the search tool and 'Write to fields of listed' or by deleting these fields).

After successful re-alignment the field 'codon_start' will be set to '1' if

  • it already existed before or
  • if ARB was able to strictly determine a content for the field 'transl_table' (which will also be written in that case).

If the re-alignment was possible using two or more different translation tables neither 'transl_table' nor 'codon_start' will be written.

 

NOTES

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

No bugs known