Submit Targeted Sequence Flatfiles with Webin-CLI


Submission of targeted sequences may be done using Webin-CLI as described in this page’s parent page: How to Submit Targeted Sequences. The native format for annotated sequences in ENA is the EMBL flat file format. You may prepare your annotated targeted sequences in this format and submit them directly to us, subject to them passing validation.

Because of the highly flexible nature of the format and the diversity of sequences which may be submitted in it, this page does not provide prescriptive information on how to prepare your file, but lists some useful resources.

Tips On Preparing Your File

If you are not familiar, please see an example of the EMBL flat file format. When you have completed your file, you must compress it with GZIP or BZIP2.

Flat File Direct Preparation

When preparing a flat file using the above example, note a few things:

  • The sections which read ‘XXX’ will be automatically filled by our pipeline on submission, and anything you write here will be overwritten

  • Information on centre name and address, and author names, is autofilled into the ‘RX’ lines (RN, RP, RA, etc.)

    • Anything you write here will not be retained, and will be overwritten by the centre and contact information associated with your Webin account, so please ensure this is correct before you submit

  • The feature table section (FT lines) are where your annotation should be inserted

    • The first column of the feature table should name the ‘feature’, e.g. source, gene, intron

    • Each feature need only be named once: following lines are treated as part of the same feature, until a new feature is named

    • The second column names qualifiers which provide information about the feature and starts with a ‘/’ character, e.g. /organism, /gene, /product

  • Each sequence entry must contain exactly one source feature, which names the biological origin of the record

    • This must include one /organism qualifier which must match with the scientific name of a species-rank taxon in the NCBI Taxonomy database

    • See tips for sample taxonomy for help with how to identify an appropriate name

  • A flat file may contain multiple sequence records, which should be separated within the file by a single line which contains only //

Flat File Preparation Resources

There are various tools which can help you with the preparation of your flat file, some of which are listed in our Third Party Tools page.

Entry Upload Templates

Some flat file templates are provided at the linked page which may help with the preparation of your submissions. These are different from the spreadsheet-based templates available from the Webin Portal, described elsewhere in this documentation, as these ones still require you to prepare your sequence records in flat file format.


This is where we provide a comprehensive directory of the available features and qualifiers you may use in your flat files, as well as information on how they should be used.

Webin-CLI Validator

When you submit your flat file you will do so via Webin-CLI. The above links back to the parent of this page which describes submission of flat files via Webin-CLI. This tool includes a validation mode able to point out errors in your file which would prevent it from being submitted. While being valid may not be the same as being complete and well-annotated, this is a useful check which may highlight some errors.


If you have your annotation in GFF3 format already, this tool created by staff at NBI Sweden can be used to convert to EMBL flat file format. Read more in the Third Party Tools page.


For multiple sequence alignments in NEXUS format with annotation, this tool is available for conversion to EMBL flat file format. Read more in the Third Party Tools page.