cDNA Sequence Submission Guidelines from the GDB

The purpose of this submission procedure is to ensure that the relevant information appears in dbEST and GDB without requiring submission to both databases. In summary the submission procedure consists of a usual submission to dbEST where the "GDB#" field in the EST File is included. The steps are:

1. Get the GDB accession id (GDBid) for the cDNA clone.

2. Create a dbEST submission including the GDBid in the GDB# field of the EST File.

3. Submit to dbEST.

By including the GDB# field in the dbEST submission, the two databases can then be linked and the information automatically integrated without having to submit separately to each database.

Submission procedure details

Each of the steps above is further explained below:

1. GDBids can be obtained for cDNA clones by using the GDB Web interface. Go to http://www.gdb.org/. Enter the cDNA clone name, for example "IMAGE:338479", into the Simple Search form and press Submit. This returns detail information about the clone including the Accession ID which in this case is GDB:1263853.

Alternatively, there are several programmatic methods for querying the database (contact help@gdb.org for more information). Also there is a flat file at ftp://ftp.gdb.org/outgoing/cDNA.Z which contains a list of all cDNA clones by GDBid and name. This file can be downloaded and used locally.

Please contact data@gdb.org if the GDBid for the cDNA clone can not be found.

2. Detailed instruction about creating a dbEST submission file can be found at http://www.ncbi.nlm.nih.gov/dbEST/how_to_submit.html

In order to link the two databases, the "GDB#" field in the EST File must contain the GDB accession id (GDBid) for the cDNA clone.

The correct syntax for the GDB# field in the example given above of IMAGE:338479 is: GDB#: GDB:1263853

3. Once the submission file is prepared, send it to batch-sub@ncbi.nlm.nih.gov

Please contact data@gdb.org if there are any questions. We will be happy to assist with your submission.

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