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ICHEC Software

Information about software packages installed on the ICHEC systems.

EMBOSS

Versions Installed

Fionn: 6.6.0

Description

EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a 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

License

EMBOSS is licensed for use by everyone under the GPL and LGPL licenses. No one individual or institute 'owns' the code. More about the licenses used can be found at http://emboss.sourceforge.net/licence/

Benchmarks

N/A.

Additional Notes

To use EMBOSS load the relevant environment module:

module load bio emboss/intel/6.6.0

The EMBOSS applications are all serial and should be run on the command line, however jobs can be run in parallel using taskfarming (see https://www.ichec.ie/support/documentation/task_farming). Jemboss is not enabled on fionn.

More information can be obtained from http://emboss.sourceforge.net/

How to cite EMBOSS:

Rice P., Longden I. and Bleasby A. (2000)
EMBOSS: The European Molecular Biology Open Software Suite
Trends in Genetics 16(6): 276-277

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