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.


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: