E.1. EMBOSS Programmatic Interfaces

Programmatic interfaces to EMBOSS are described below.


The list of interfaces is by no means comprehensive. If you know of other relevant interfaces to EMBOSS please email emboss-bug@emboss.open-bio.org with details.

The available programmatic interfaces include:



Various modules utilise the EMBOSS programs.



A Perl interface to the EMBOSS libraries allowing you to write perl programs that look and feel like a typical EMBOSS program.

BioPerl class for EMBOSS Applications Bio::Tools::Run::EMBOSSApplication


The EMBOSSApplication class can represent any EMBOSS application. It is created by a Bio::Factory::EMBOSS object which primes it by reading an application ADC file.

BioPerl EMBOSS application factory class Bio::Factory::EMBOSS


The EMBOSS factory class encapsulates access to existing EMBOSS programs.

BioPerl class for EMBOSS application qualifiersBio::Tools::Run::EMBOSSacd


The EMBOSSacd class represents all the possible command line arguments that can be given to an EMBOSS application.



MOBY is a ontological system for interoperability between biological service providers whether they be data hosts or analytical services. The EMBOSS applications have been incorporated.



Soaplab generates Web Services for command line programs. Two types of Web Services interface (generic interface and typed interface) are possible. The generic interface allows input data to be sent as weakly typed name-value pairs. This allows diverse applications to be integrated under a single programming interface. The typed Web Services interface has input/output type descriptions defined at WSDL/XSD level which allows Web Service clients to check input/output data types using standard means.