NCBI logo FTP site
PubMed Entrez BLAST OMIM Books TaxBrowser Structure
  Search for


NCBI
back to NCBI homepage
back to NCBI homepage
SITE MAP
Guide to NCBI resources


About NCBI
The science behind our resources. An introduction for researchers, educators and the public.

GenBank
sequence submission support and software

Molecular databases
sequences, structures and taxonomy

Literature databases
PubMed and OMIM

Genomic Biology
the human genome, whole genomes and related resources

Tools
for data mining

Research at NCBI
people, projects, and seminars

Software engineering
 Tools, R&D and databases

 Education
teaching resources and on-line tutorials

FTP site
download data and software

Contact information
 how to reach us

How to uncompress *.gz and *.Z files

Files available from the NCBI anonymous FTP site have been compressed using the "gzip" program (and have the extension *.gz), or the UNIX "compress" program (and have the extension *.Z). This document describes how both file types can be uncompressed.
  1. uncompress *.gz files
  2. uncompress *.Z files
    1. UNIX
    2. PC
    3. MAC
  3. compression newsgroup FAQs

Uncompress *.gz files back to top

As announced via the GenBank newsgroup on June 15, 2000, NCBI now uses the gzip compression utility instead of the Unix "compress" utility for all GenBank files, starting with GenBank Release 119.0.

Comparisons of gzip to compress for simplistic sequence data (e.g., EST, GSS, STS) yielded an additional 50% reduction in the size of a compressed file. Given that ESTs and GSS sequences comprise a huge portion of the GenBank data NCBI distributes, switching to gzip saves a great deal of disk space, and reduces the amount of bandwidth utilized by those who ftp GenBank files.

As a result of the switch to gzip, file naming conventions have changed. The suffix of compressed GenBank data files was previously ".Z" . After the switch, the suffix became ".gz" .

The gzip utility is used to compress various other data on the ftp site as well.

If you are unsure about the availability of gzip for your platform, please contact your system administrator. If you find that the utility is not installed, one possible place for obtaining gzip is:

http://www.gnu.org/software/gzip/gzip.html

Uncompress *.Z files back to top

Files with a *.Z extension have been compressed by the UNIX "compress" program. Those files can be handled with the Unix "uncompress" program, or programs such as the PC and Mac utilities described below.

UNIX back to top

If you are using a UNIX workstation, use the uncompress program to expand the files to their original state.

PC back to top

If you are using a PC, you will need two programs (pkunzip & comp430d.zip) in order to uncompress a *.Z file.

If you do not already have the pkunzip program on your PC, please contact your systems administrator to obtain it, or search the Net to find a Web site from which you can download that program.

The "comp430d.zip" freeware program is available from the "pub/dab" directory the NCBI anonymous FTP site (ftp://ftp.ncbi.nih.gov/pub/dab/). It allows you to decompresses Unix ".Z" files under DOS.

Once you download the "comp430d.zip" file, follow these steps:

  1. Run the "pkunzip" program to unzip "comp430d.zip."
    Use the command:
    pkunzip -d comp430d.zip

  2. Rename the "comp430d.exe" file to "compress.exe" with the following command:
    ren comp430d.exe compress.exe

  3. Copy the "compress.exe" to "uncomp.exe" using the following command:
    copy compress.exe uncomp.exe

  4. run the uncompress program:
    uncomp.exe
    E.g., uncomp.exe omim.txt.Z

    Or, you can leave off the ".exe" portion and simply type the command:
    uncomp
    E.g., uncomp omim.txt.Z

MAC back to top

If you are using a Mac, you can search the Web to find sites that have a program such as "MacCompress," which handles files that have been prepared with the Unix compress program.

One example web site that provides information about various Mac compression/uncompression programs is: A search of the web for terms such as "Mac" and "compress" will find other sites as well.

The Apple home page (http://www.apple.com/) and the Apple Support page (http://www.apple.com/support/) might also provide information about compression and uncompression of various file types on the Mac.

Compression Newsgroup FAQs back to top

You can find additional information about compression/uncompression utilities on the Compression Newsgroup. They provide an archive of Frequently Asked Questions (FAQs) at:

http://www.faqs.org/faqs/compression-faq/

You might also search the web to find sites that provide compression/uncompression software for various platforms.

Revised June 3, 2002