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Last update on 04. Mar 2022 .
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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:

Transfer will always happen from source to target species (i.e. from left to right side).
Select the transfer mode:
  • "whole species" will copy all fields,
  • "single field" will copy one single field (selectable, allows to append data) and
  • "using FTS" will use the "field transfer set" selected below (see ´Field transfer sets´).
    The "using FTS" mode has two flavors (with and w/o sequence data; see section below). The second mode can be used to update/synchronize metadata between two databases containing different alignments (e.g. update metadata of common species from a new SILVA release into your local databases).

Select the transfer scope:
  • "selected species" will copy (from) the selected species into a new species or to the species selected in the right-side hitlist.
  • "listed species" will copy all species listed in the left-side hitlist.

Click the 'Transfer species' button in the window center to transfer according to selected transfer-type and -scope.
See ´Save Database´ for howto save the modified database(s).
 

Overwritten data  

This section describes when and what data will be overwritten and when data gets mixed into existing data.

In "whole species" transfer mode

  • any existing species (with the same ID, i.e. 'name') will be deleted and
  • a full copy of each source species will be created.

The "single field" and "using FTS" transfer modes

  • will copy from the selected source species to the selected target species when "selected species" scope is used (regardless whether their IDs match or not) or
  • will copy from each listed species to (a new or already existing) target species with the same ID.

Some fields are handled special:

  • the 'name' entry will always be transferred when missing at target.
  • the 'acc' entry will be transferred when missing at target (and when "using FTS" mode).
  • whether 'ali_*/data' entries (i.e. the sequence data) will be transferred, depends on the transfer mode:
    • "whole species" and "using FTS (with seq)" will transfer all existing sequence data
    • "single field" and "using FTS (w/o seq)" will not transfer any sequence data

  • all transferred sequence entries will be targeted by alignment adaption (see below).

 

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  

You may mix data from source fields with data of existing target fields using FTS as follows:

For example if you have a source field 's1' and an existing destination field 'd1' you may merge the contents of these fields (into 'd1') using a simple rule transferring 's1' to 'd1' and add one of the following ´ARB Command Interpreter (ACI)´ expressions:

ACI                   does
dd;readdb(d1)         prefix content of 's1' in front of 'd1'
dd;" ";readdb(d1)     dito, but insert one space
readdb(d1);dd         append content of 's1' behind 'd1'
readdb(d1);" ";dd     dito, but insert one space
 

EXAMPLES  

For general examples of 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.

Entries in the target database will be overwritten w/o further consent (applies to single transferred fields and complete transferred species).

 

BUGS  

No bugs known