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Last update on 04. Apr 2019 .
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Compare and Transfer Species Entries

OCCURRENCE

ARB_MERGE/Transfer species

 

DESCRIPTION

Allows

  • database searching,
  • comparison of the two databases,
  • transferring data from left to right
  • realigning sequences to new alignment

Database Searching:

To perform database searching within the individual databases use the left or right part of the 'TRANSFER SPECIES' window for source and target database (DB), respectively.
The database is scanned for 'species' (see ´Glossary´) which contain (or do not contain) the search string within the specified 'field' (see ´Glossary´). The corresponding 'species' and the respective 'field' entries are listed in the 'HIT LIST' subwindow. The number of hits is displayed after the 'Hits:' prompt.
Define whether matching or non matching species should be listed by pressing the appropriate combination of left and right buttons in the 'QUERY TYPE' area. Performing multiple searches, define whether the list of 'species' should be replaced by the new results, whether newly found 'species' should be removed from or appended to the existing list.
Select a 'field' from the 'Fields' subwindow.
Type the search string to the 'Search string' subwindow.
Press the 'RUN QUERY' button of the results area.

Data Transfer:

To transfer a single 'species' and all its 'field' entries, select the species from the list displayed in the 'HIT LIST' subwindow and press The 'TRANSFER SELECTED SPECIES' button in the middle column of the 'TRANSFER SPECIES' window.
To transfer all listed 'species' and all corresponding 'field' entries, press the 'TRANSFER ALL LISTED SPECIES' button in the middle column of the 'TRANSFER SPECIES' window.
To transfer the entries of a 'field' selected from the 'Search field' subwindow for all listed 'species, press the 'TRANSFER A FIELD FOR ALL LISTED SPECIES' button in the middle column of the 'TRANSFER SPECIES' window (see ´Transfer one field of listed species´).
See ´Save Database´ for howto save the modified database(s).

Adapt Alignment:

ARB Merge tries to keep the alignment correct. Normally people have inserted new gaps in either the left or right database. By entering the ID(s) of some reference species in the input box in the upper center of the TRANSFER SPECIES window, the program will try to find those species in both databases, create a column reference list, and realign all transferred sequences. To enable this feature, enable the 'Adapt alignment' toggle.
 

NOTES

None

 

EXAMPLES

For examples for database searching see ´Search Database for Species´.

 

WARNINGS

The data will always be transferred from the source DB to the target DB. If you want to align sequences during transfer, it is recommended that the left database has fewer gaps than the right one.

If there are entries (for selected data) in both databases, those in the target DB will be overwritten!

 

BUGS

No bugs known