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.