source: trunk/HELP_SOURCE/source/sp_IDs.hlp

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#************* Title of helpfile !! and start of real helpfile ********
TITLE           ARB NAMESERVER / Synchronize IDs

OCCURRENCE      ARB_NT/Species/Synchronize IDs
                ARB_MERGE/Check IDs/Synchronize

                It's also used by several functions that create new species (eg. after import).

DESCRIPTION     Automatically creates unique identifiers (=shortnames stored in field 'name') for
                species entries in the database.
                It is required for ARB that all species have different, unique IDs - otherwise
                ARB will misbehave in many ways!

                The single species entries are normally distinguished and identified by their
                accession numbers.

                The unique IDs are created using information from the 'full_name'.

                  Usually, the first three letters are taken from the genus designation,
                  the remaining letters from the species name.

                These tasks (identification and ID-generation) are handled by the
                so called NAMESERVER.

                If there are duplicated (ie. indistinguishable) species entries,
                the different versions are indicated by appending a dot followed
                by running numbers: e.g. "DicTherm.2", "DicTherm.3", ...

NOTES           The IDs are stored with the database. They are protected versus change
                to avoid assigning the same ID to different species.

                Accession numbers (stored in the field 'acc') normally will be imported
                from public databases together with the sequence data.
                If no accession number has been found during import (eg. because the sequence
                has not yet been published), ARB will automatically generate accession
                numbers (="ARB_" followed by a CRC-32-checksum of the sequence data).

SECTION         Duplicate IDs

                "Synchronize IDs" will create duplicate names whenever it fails to distinguish
                between two or more species.
                If there is some warning about duplicate entries, you REALLY should try
                to understand the reason why this happens!

                Following some situations where you will run into that problem and
                instructions how to solve the problem:

                 1. you've imported multiple IDENTICAL sequences w/o accession number. The
                    accession numbers generated by ARB will be identical as well and
                    "Synchronize IDs" will complain about duplicate species.

                    Consider to remove the duplicated species. Normally duplicated information
                    isn't very useful. If this is no option for you, you might as well manually
                    change the accession numbers of the duplicated species (if you understand
                    the implications).

                 2. you've imported several genes from one organism and each of them
                    was assigned the same accession number (the acc of the organism)

                    Use an additional field to make your species entries distinguishable
                    (e.g. a field containing the start-position of each gene).
                    You may configure whether and which field to use together with
                    NAMESERVER (see LINK{namesadmin.hlp}).

SECTION         NAMESERVER

                The NAMESERVER stores the associations between the unique IDs and
                species entries (represented by the accession number and optionally
                an additional field) in the NAMESERVER-database. The standard nameserver
                uses the file '$ARBHOME/lib/nas/names.dat' as its database.

                For more details refer to the active arb_tcp.dat (Tools/Nameserver admin/Configure arb_tcp.dat).

                If you have multiple database containing common species, synchronizing IDs for
                all these databases will generate the identical IDs for
                identical species (as long as you use the same NAMESERVER-database).

SECTION         Central NAMESERVER

                It is possible to link names.dat to a central names.dat, but you should
                be aware, that there may occur temporary inconsistencies, if multiple users
                use the NAMESERVER at the same time.

                The NAMESERVER examines names.dat and terminates within 5-10 seconds if
                the file changes. A message is written to the console window in either case.

                Another way to use a central NAMESERVER is to edit '$ARBHOME/lib/arb_tcp.dat'
                and to specify a central host for ARB_NAME_SERVER.
                This completely avoids any inconsistencies, but if too many users try to access
                that nameserver at the same time, you'll run into DOS problems.

EXAMPLES        None

WARNINGS        None

BUGS            No bugs known