Project setup

To establish a working setup for genome project, we suggest to follow the protocol outlined below.

1. Both parties sign a cooperation agreement (see License page).
2. The external project partner will declare one project leader (herein User) as primary contact.
3. User sends us the sequence data via email or snail mail. (Please note: We solely use encrypted connections within GenDB, if you send your data via email, please make sure that you encrypt it.)
4. We will set up a project in the GenDB system (please suggest a name) and generate a mailing list for this project under the same name. The User can control access to the project (via GPMS).
5. We will run the automated gene calling pipeline (Reganor). (Please note: The sequences do not need to be in one contig, but the higher the number of contigs, the more genes will be missed and the more artifacts will occur during the gene prediction.)
6. Both parties will check the results of the automatic gene calling. If needed, we will adapt the parameter settings.
7. We will run the pipeline for functional annotation (Metanor) using a number of tools. The User should interact in tool and parameter definition. Among the tools are:
   • Blast vs. SwissProt
   • Blast vs. KeGG
   • Blast vs. COG
   • InterPRO-scan
   • HMMer search vs. Pfam and TIGRFAM
   • TMHMM
   • Signal-P
   • helix-turn-helix
   • project specific tools (e.g. Blast vs. another related genome)
8. Both parties will check the results of the automatic functional annotation.
9. After consultation of both parties and possibly polishing of the sequence, the manual annotation can proceed.
10. The User creates individual accounts for all members of the annotation team (optional) (via GPMS). Please note: We usually provide a training course for all members of the manual annotation team (optional).
11. We will export the annotation to EMBL/GenBank format.
12. We (or User) will perform the submission to sequence databases (on request).
13. The sequence can remain in GenDB for further annotation (or be deleted on User request).
14. The User can determine the modes of access to the GenDB web interface, e.g. providing a web site as additional information to the paper.