Chapter 12. EMBOSS

EMBOSS (European Molecular Biology Open Software Suite) is an open source package of sequence analysis tools. This software covers a wide range of functionality and can handle data in a variety of formats. Extensive libraries are provided with the package, allowing users to develop and release their own software. EMBOSS also integrates a range of currently available packages and tools for sequence analysis, such as BLAST and ClustalW. A Java API (Jemboss) is also available.

EMBOSS contains around 150 programs (applications). These are just some of the areas covered:

  • 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.

. . . and much more.

For details, see Section 12.4 at the end of this chapter.

We're using Version 2.5.0 of EMBOSS.

Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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