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Sequin Entrez BLAST OMIM Taxonomy Structure

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GenBank Submissions Handbook

Sequin 12.21 is now available.

What Is Sequin

Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissions containing long sequences, multiple annotations, gapped sequences, or phylogenetic and population studies. A single Sequin file should contain less than 10,000 sequences for maximum performance. Larger submissions should be made with tbl2asn . Getting Started with Sequin is a brief overview of the program.

How to Get Sequin

Sequin 12.21 is currently available from the NCBI. Sequin runs on Macintosh, PC/Windows, and UNIX computers. Instructions for downloading and installing the program are provided. The program itself, along with its on-line help documentation, is available by anonymous FTP.

A Quick Guide to Sequin

This demonstration of how to use Sequin is derived from the August 1996 issue of the NCBI News and includes a section on how to prepare your sequence data files before you begin preparing your sequence submission with Sequin.

Sequin Help Documentation

A window containing the Sequin Help Documentation is opened when the Sequin program is launched. The contents of this scrolling window change as you move within the Sequin program, presenting you with help documentation appropriate for the section of Sequin you are presently visiting. This documentation is also available in a World Wide Web format. Detailed instructions for the various Sequin Wizards are also available.

Annotation Using A Table

A five-column, tab-delimited table of feature locations and qualifiers can be used to import annotation into an existing Sequin submission. This is the same table format that must be used to annotate features when creating a submission using tbl2asn.

Network-Aware Sequin

Sequin can be used in one of two modes, stand-alone or network-aware. In the network-aware mode, the program can exchange data between any computer connected to the Internet and the NCBI.


The SequinMacroSend tool allows the submission of very large Sequin files directly. Those files that may be truncated during mailing with conventional maile rs, including large population sets or complete plasmids or small genomes, can be sent using this method.

Sequin Update Notification

To receive email notification about updates to Sequin, as well as a description of what is included in the update, follow these directions.


The tbl2asn command line program is available via ftp and is designed as an alternative to the Sequin program for generating large single submissions (complete genomes) containing a great deal of annotation. It can also be used to generate a batch submission containing thousands of individual sequences. More detailed instructions about using this function are provided. When submitting a complete bacterial genome, please review the genome guidelines.

Sequin Revision History

The Sequin revision history contains a reverse chronological list of changes made to the Sequin program.


Questions or Comments?
Write to the NCBI Service Desk

Revised June 20, 2012.