1. Application

Please apply for your submission through “Application form for MSS”.According to your application, DDBJ MSS sends you how to use MSS via an email.

Preparation for sequence data submission

When your data are corresponding to the following cases, please register BioProject and BioSample before using MSS.

• whole genome-scale sequence:
  • Complete genome, nearly complete genome and draft genome (WGS, HTG).
  • Excluding sequence data consisting only of organelle, virus/phage or plasmid sequence(s).
• transcriptome: TSA (Transcriptome Shotgun Assembly), EST
  • It is also required to submit non-assembled data (original reads, or the alternative) to DRA before TSA submission.
  • In the case of EST, BioProject and BioSample are not required, but recommended.
• TLS (Targeted Locus Study)

Description of annotation

• For whole genome-scale sequence, it is optional to describe biological features except source and assembly_gap. However, in case of highly novel species, i.e. not available any sequence data, it is required to describe feature annotation for at least one genome as a representative.
• If you decide to submit a genome with annotation, it is required to reserve locus_tag prefix on BioSample submission.
• For feature annotation of prokaryotic genome, we recommend to use DFAST (DDBJ Fast Annotation and Submission Tool).
• For TSA data, it is optional (basically unnecessary) to describe biological features except source and assembly_gap.
• In the case of EST, you can not describe any biological features except source.

2. Make submission files

Submission files required for MSS

Sequence file

The text file that contains all nucleotide sequences in FASTA-like format.

Details : Submission file format：Sequence file.

Annotation file

The tab delimited text file that contains your data other than sequences, such as submitters, references and biological features.

Details : Submission file format：Annotation file.

AGP file （in case of CON entries）

The tab delimited text file of nine columns that contains your data , such as the order and orientation of the piece entries to construct CON entry.

If you can build a sequence from an AGP file, you do not need a sequence file.

Details : Submission file format： AGP file.

Check submission files

Before submitting to DDBJ, the files should be checked with software tools provided from DDBJ.

UME (Utilities for MSS file Error check)

You can verify the syntax, format and amino acid translation of CDS features of Sequence file and Annotation file. UME includes both Parser and transChecker.

OS : Windows, Unix/macOS

Details : UME User's Manual.

Parser

You can verify the syntax and format of Sequence file and Annotation file.

OS : Unix

Details : Parser User's Manual.

transChecker

If your data include CDS features (protein-coding sequence), you can validate the amino acid translation.

OS : Unix

Details : transChecker User's Manual

• The DDBJ check tools do not have any function of making nor editing submission files. Therefore, prepare your submission files by using software such as text editor, spreadsheet etc.
• Do not send such submission files with errors detected by the check tools. You should send your files to DDBJ after you completely fix the errors.
• If you describe CDS feature(s) in your annotation file, you should validate it with UME or transChecker.
• Before installing the check tools, check End-user license agreement.

3. Review the submission files

After validating the sequence and annotation files by using the check tools, send them to DDBJ.

• Before preparing the entire sequence and annotation files, you can send a part of your data as a trial basis and then ask DDBJ whether the submission files are correctly created or not. (This step can be omitted).

DDBJ reviews submission files and then informs the submitter of some correction requests and/or inquiries.
If there is no problem with the contents of the file, DDBJ will issue accession number(s) for your data and acknowledge the accession number(s) to the contact person by email.