2. Using EMBOSS

EMBOSS includes a comprehensive set of sequence analysis programs and integrates other popular publicly available packages and tools via the EMBASSY section. Every application has the same style of command line interface. This means that once you master one program you'll have mastered them all. Powerful graphical interfaces and easy to use web-based interfaces are available. In addition, the applications are integrated with powerful workflow software, for linking multiple applications and data sources together into analysis pipelines.

All common file formats for molecular sequences, sequence features and sequence alignments are supported. EMBOSS uses consistent methods for specifying these data; the Uniform Sequence Address (USA) for sequences and alignments and Uniform Feature Object (UFO) for features. Data may be kept in a local file or database, retrieved by some other program, or sit on a remote server on the Internet. Powerful database indexing software are included to provide rapid access to your own data. Databases and access methods are defined in a configuration file which is easy to edit for new sources of data and access methods. EMBOSS detects the format of an input sequence automatically. Many other common data formats are handled automatically, saving you a great deal of hassle when using the applications.

The options and command line behaviour of each application is defined in a text file called the AJAX Command Definition (ACD) file. This allows the programs to be customised without any programming knowledge. For example, it is trivial to set a default value or constrain the types of an input sequence. Applications are well documented, including validated usage examples, allowing you to see clearly how an application is used in practice. Comprehensive documentation is also available from the EMBOSS website.

EMBOSS users are very well supported. Mailing lists for discussions and for reporting bugs are well used, and you can expect timely support from the core developers and a large user community. All bug reports, and requests for support and new features are logged and tracked so you can rest assured that action will be taken as soon as possible.