Trends in Genetics
ResourceEMBOSS: The European Molecular Biology Open Software Suite
Section snippets
Data sources
Sequence data can be used in any of the common sequence formats, with new formats easily added. For institutes where the public sequence databases are installed, EMBOSS can use these with a choice of formats, including GCG (Wisconsin Package Version 10, Genetics Computer Group, Madison, WI, USA; http://www.gcg.com/), SRS (Ref. 2), STADEN (http://www.mrc-lmb.cam.ac.uk/pubseq/), ACEDB (Ref. 3, see http://www.acedb.org/) and BLAST databases4. Failing this, individual sequence entries can be
The user interface
The basic interface is the command line. This is needed for many reasons, including the ability to run applications as part of larger automated analyses. The command line is defined in ‘ACD’ definitions (http://www.sanger.ac.uk/Software/EMBOSS/Acd/).
Most of the more friendly user interfaces in bioinformatics are simple forms which build the command line for the user, run the program, and present the results. EMBOSS is easy to convert to these interfaces by using the ACD definitions to generate
EMBOSS for developers
Fashions change in bioinformatics, and a number of programming languages have been favoured. In EMBOSS we have chosen to use standard C but we also support development in other languages. The first of these are from the Birkbeck Template Library (http://www.cryst.bbk.ac.uk/∼classlib bioinf/BTL99.html). The licensing is open source (Gnu General Public Licence; http://www.gnu.org) so that EMBOSS is freely available. The software libraries are under the library GPL to allow other packages to link
Applications
The original goal of EMBOSS was to re-implement applications in the ‘EGCG package’ (see http://www.uk.embnet.org/embnet.news/vol3_1/software.html)5 of extensions to GCG. This has now been achieved, with all the popular EGCG applications either replaced by EMBOSS or by other free software.
Additional applications have been contributed by several EMBnet members with their own development groups. The major contributors to date have been the UK node at Human Genome Mapping Project in Hinxton,
Releases
The first developers’ release was in the summer of 1998, together with an EMBnet workshop to review developments. The full beta-test release was made available in summer 1999, with a second EMBnet workshop where user feedback was gathered. We have implemented most of the recommendations from that workshop, and the first official release of EMBOSS followed in Spring 2000. The latest details are available from the EMBOSS Web pages (http://www.sanger.ac.uk/Software/EMBOSS/).
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