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functionality of GCG and EGCG. New EMBOSS programs are added and current programs
continuously improved.
Once a fully commercial package, the GCG license became much more expensive.
Institutions such as the RFCGR 2 had to raise or introduce academic user fees for the use of
the GCG package. In contrast, EMBOSS is a totally free package, downloadable from
http://emboss.sourceforge.net/download/
Cost considerations, together with a requirement for energetically developing
contemporary analysis software have encouraged many institutions to move towards
EMBOSS. As the two packages share an overall structure and comparable G raphical U ser
I nterfaces (GUIs), experienced GCG users found little difficulty running EMBOSS from
the UNIX command line or from behind its various GUIs.
Again, in similar fashion to GCG, EMBOSS includes a number of well established
programs not written especially for EMBOSS. Examples of such programs include
clustalw for multiple sequence alignment ( emma in EMBOSS) and primer3 for primer
design ( eprimer3 in EMBOSS). This policy is clearly preferable to trying to rewrite tools
that are accepted as “the best” by the user community. Programs imported in this fashion
are run behind a software wrapper that gives them a look and feel compatible to the core
EMBOSS programs.
One of the major features not yet to have been implemented in EMBOSS is a
sequence database similarity search tool such as blast . Currently, similarity searches must
be conducted elsewhere before the results are analysed using EMBOSS tools.
2.
EMBOSS - A Free Open Software Suite
2.1
Overall structure
The pre-requisite of designing EMBOSS was that the source code be freely available to all.
Software developers should be permitted to access to the code and to manipulate it in
whatever fashion they chose. All users should be able to access the extensive (currently
more than 200) collection of EMBOSS applications from anywhere in the world at no cost.
Access via intuitive web sites (and other forms of GUI) is of particular importance.
EMBOSS, following the structure of GCG, is comprised of many small programs
each carrying out a single task. This has proved to be of particular benefit to bioinformatics
specialist wishing to create larger applications by “stitching together” the simple EMBOSS
applications. However, this structure is not always ideal for the less ambitious user. In
particular, determining the name of the program appropriate for a given task is not always
easy for the more casual user.
For the user already familiar with GCG, a table of GCG/EMBOSS program
equivalencies has been constructed at several sites. Some of them can be found at:
x http://www.sanbi.ac.uk/mrc/GCG_replacement.html
x http://www.biobind.com/faq/gcg-emboss.html
x http://helix.nih.gov/apps/bioinfo/emboss-gcg.html
Not every EMBOSS program will have an exact GCG equivalent, but functionality
should be reproduced.
Also, a small utility called wossname is also provided to act as a dynamic index of
programs within the EMBOSS suite (The Jemboss GUI offers users a more powerful
keyword search). The program uses keywords to identify EMBOSS programs pertinent to a
2 Rosalind Franklin Centre for Genomics Research (UK), situated near Cambridge. This used to be the
Human Genome Mapping Project Resource Centre (HGMP-RC)
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