The NCBI Structure Group
ASN.1 file format

ASN.1, or Abstract Syntax Notation One, is an International Standards Organization (ISO) data representation format used to achieve interoperability between platforms. NCBI uses ASN.1 for the storage and retrieval of data such as nucleotide and protein sequences, structures, genomes, PubMed records, and more. It permits computers and software systems of all types to reliably exchange both the data structure and content.

The documentation for the NCBI Software Development ToolKit contains information about the ASN.1 specification. The toolkit documentation is quite large (over 300 pages) and can be downloaded as the MS Word file sdk.doc.Z from the NCBI FTP site. Please see the readme file in that directory for more information.

The NCBI Software Development ToolKit (known as the "NCBI Toolbox") is a set of software and data exchange specifications used by NCBI to produce portable, modular software for molecular biology. The software in the Toolbox is primarily designed to read ASN.1 format records. It is available to the public in the toolbox/ncbi_tools directory of NCBI's ftp site, and can be used in its own right or as a foundation for building tools with similar properties. The readme files in the toolbox and toolbox/ncbi_tools directories of the FTP ste contain more information about the toolbox and ASN.1.

The following publications might also be of interest:

  • Ostell, J.M. 1995. Integrated access to heterogeneous biomedical data from NCBI. IEEE Eng. Med. Biol. 14, 730-736.

  • Ostell, J.M. 1996. The NCBI software tools. In Nucleic Acid and Protein Analysis: A Practical Approach, M. Bishop and C. Rawlings, Eds. Oxford: IRL Press, pp. 31-43.

  • Ostell, J.M., Wheelan, S.J., and Kans, J.A. 2001. The NCBI data model. Chapter 2 in Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 2nd ed., edited by Baxevanis, A.D. and Ouellette, B.F.F. New York: John Wiley & Sons, pp. 19-43.
    (The chapter primarily describes the structure and content of the NCBI data model and its implications for biomedical databases and tools. However, there is a brief description of ASN.1 on p. 23, and refers readers to the 1995 article noted above for more detail.)

If you have questions about ASN.1 or the toolkit after reviewing these publications, you can contact

Finally, there are a number of external WWW sites, such as the ones below, that provide additional information about ASN.1:

Revised 18 September 2016