sequin

Describe ANSI escape sequences from a string

$ printf "[\x1b[38;5;4mCiao, \x1b[1;7mBaby.\x1b[0m\n]" | sequin

$ ls -l --color=always | sequin

$ cat [path/to/file.golden] | sequin

$ sequin -- [ls -l go.*]

$ git -c status.color=always status -sb | sequin -r

sequin [options] [file]

sequin
    Launches the Sequin graphical user interface application without loading a specific file.


sequin filename
    Launches Sequin and attempts to open the specified filename. Typically, this would be an existing .sqn (Sequin flat file) or .fsa (FASTA) file for editing or viewing.


-help
    Displays a brief help message detailing available command-line usage information for the application.


-version
    Outputs the version information of the Sequin application to the console.

The NCBI Sequin is a standalone software application developed by the National Center for Biotechnology Information (NCBI) for preparing and submitting sequence data to the GenBank, EMBL, and DDBJ sequence databases. It provides a comprehensive graphical user interface (GUI) environment for annotating, editing, and validating DNA and protein sequence records before submission. Users can input raw sequence data, add feature annotations (such as genes, coding regions, mRNA, etc.), correct errors, and ensure the data meets submission standards. Sequin plays a critical role in the biological research community by facilitating the deposition of new sequence discoveries, making them publicly available for researchers worldwide. While primarily a GUI tool, it can be invoked from the Linux command line to launch the application or open specific files.

Sequin is primarily a graphical user interface (GUI) application designed for interactive data preparation. It is not a command-line utility for automated script processing like many standard Linux commands (e.g., grep, awk). Its command-line options are limited mainly to launching the application or opening files, and it does not offer extensive command-line functionality for batch processing. For programmatic submissions or automated annotation, other NCBI tools like tbl2asn are often more appropriate. Installation typically involves downloading and extracting a distribution, rather than being part of standard Linux package repositories.

Sequin primarily works with FASTA (.fsa) format for raw sequence input and generates its own native .sqn (Sequin flat file) format for saved submissions. It can also import and export other common bioinformatics formats to some extent, facilitating data exchange within the scientific community.

Once a sequence record is prepared, validated, and annotated in Sequin, the application guides the user through the final steps of submitting the data directly to the NCBI. The submitted data then undergoes further review and processing before being accessioned into GenBank, EMBL, or DDBJ, making it publicly available.

Developed by the National Center for Biotechnology Information (NCBI), Sequin was introduced to address the growing need for a user-friendly tool to facilitate the submission of biological sequence data to GenBank. Over the years, it has undergone several revisions to accommodate changes in data submission standards, add new annotation features, and improve user experience. Its development paralleled the exponential growth of genomic sequencing, becoming a cornerstone tool for researchers to share their sequence discoveries with the scientific community. While newer web-based submission methods exist, Sequin remains a robust option, particularly for complex submissions and for those who prefer a desktop application.

tbl2asn(1), makeblastdb(1), blastn(1), sra-tools(1)