Google
More docs on the ARB website.
See also index of helppages.
Last update on 25. Nov 2018 .
Main topics:
Related topics:

NAMESERVER ADMIN

OCCURRENCE

ARB_NT/Tools/Name server admin

 

General warning

Most of the functions here will destroy or at least affect the consistency of the species IDs (shortnames) for all users of the affected names.dat.

Please only use these functions if you really know what you are doing. Otherwise ask your local ARB guru.

 

DESCRIPTION

Delete old names file

After using the NAMESERVER for a while, the names database may contain several entries which are used nowhere.
This happens e.g. if you've changed accession numbers during your data curation or if you had species in one of your database which you don't store anymore.
To get rid of these unused IDs click 'Delete old names file'. Your names database will be deleted and all IDs will be regenerated.

Edit names file

The names database is a simple text file, which may be modified with a texteditor.
Use this feature with care!

Remove ARB_XXXX entries

ARB automatically generates accession numbers if they are missing. e.g if you import plain sequence data.
Use this to get rid of all NAMESERVER entries using ARB_xxx accession numbers.

After using any of the above functions

you should consider to synchronize IDs (see ´Synchronize species IDs´) in all your arb-databases.

Additional species ID field

If you have good reasons, why you have to keep several species with identical accession numbers in your databases, you'll normally get problems with the ARB NAMESERVER, because it handles these species as "identical" and gives them IDs like 'HalHalob.2', 'HalHalob.3' etc. to mark them as duplicates.
Here you can specify an additional DB-species-field, which will be used for species identification in addition to 'acc' (accession number).
This setting is database-specific - so you have to set it for each database where it's needed.
For each field you use, a separate NAMESERVER will be generated. That means:
  • You have to add a new entry into arb_tcp.dat (except for field 'start' where a predefined entry exists)
  • Names between database using different additional fields (or no add. field) are NOT compatible. To merge such databases, change this setting such that both databases use equal additional fields and synchronize species IDs. Otherwise you'll most likely merge the data of non-equal species, which will corrupt your data!

Please also read help for ´ARB NAMESERVER / Synchronize IDs´.
 

NOTES

If you comment out the default ARB_NAME_SERVER entry in arb_tcp.dat, renaming with empty 'Additional species ID field' will lead to an error. Use this to avoid creating databases that use the standard NAMESERVER with no additional field.

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

No bugs known