EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

Within EMBOSS you will find around hundreds of programs (applications) covering areas such as:

  • Sequence alignment,
  • Rapid database searching with sequence patterns,
  • Protein motif identification, including domain analysis,
  • Nucleotide sequence pattern analysis---for example to identify CpG islands or repeats,
  • Codon usage analysis for small genomes,
  • Rapid identification of sequence patterns in large scale sequence sets,
  • Presentation tools for publication

Availability and Restrictions


The following versions of EMBOSS are available on OSC systems:

Version Oakley
6.4.0 X*
* Current default version

You can use module spider emboss to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


The EMBOSS software package is available without restriction for all academic OSC users.

Publisher/Vendor/Repository and License Type

EMBnet user community, Open source


Usage on Oakley


For the Oakley system, run the following command:

module load emboss


The EMBOSS programs are typically used to perform one or more tasks on a large number of sequences.  Once the emboss module is loaded, all emboss commands are available for your use.

Batch Usage

Coming soon.

Further Reading

See Also

Fields of Science: