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Last update on 25. Nov 2018 .
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Insert / Delete using SAI

OCCURRENCE

ARB_NT/Sequence/Insert delete/using SAI

 

DESCRIPTION

Instead of running multiple inserts/deletes one by one (using ´Insert / Delete Column´), you may as well define an SAI describing at which alignment positions inserts/deletes shall happen and use this window to apply them all in one pass.

The main reasons why you might want to do that are performance reasons: during insert/delete every sequence in the current alignment has to be read, modified and written back to the database (for bigger databases this may take some minutes). Doing multiple modifications at once is nearly as fast as doing one single modification.

First define which SAI to use and how to interpret the information stored there in the upper section of the window:

  • first select all ranges or all columns,
  • select which SAI to use,
  • choose whether and define what characters to include or exclude

After doing so, the number of selected ranges or columns will refresh.

The difference between ranges and columns depends on the 'Action' you select:

  • when DELETEing there is no difference between ranges and columns. Simply define what characters may be deleted (or enter '%' to allow any characters) and press the 'DELETE' button.
  • when INSERTing gaps it does make a difference:
    • if 'columns' are selected, the specified number of gaps will be inserted infrontof/behind EACH selected column and
    • if 'ranges' are selected , the specified number of gaps will be inserted only ONCE after multiple consecutive selected columns.


 

NOTES

None

 

EXAMPLES

Use case

  • alignment curation
    To be able to correct the sequence alignment - either manually or when using ´The integrated aligners´ - you often need to insert some spare columns around alignment positions of poor alignment quality.
    To insert such extra columns, create a new empty SAI and mark all such column ranges by inserting 'XXX' into that SAI (using ´ARB_EDIT4 - Sequence primary and secondary structure editor´). Then select all ranges (in the window described here) where your new SAI contains 'X' and insert the desired amount of gaps in front of and behind all selected ranges.

 

WARNINGS

None

 

BUGS

No bugs known