Information Technology Reference
In-Depth Information
in remote databases managed on any SRS server throughout the world. This is of particular
value to users wishing to install the EMBOSS programs locally. Installing the software and
keeping it up to date is a relatively minor undertaking. Keeping a realistic range of
sequence databases up to date locally is another matter, requiring an enormous amount of
disc space and far more time than most users can afford. Remote access to sequence
databases is possible using elements of the
S
equence
R
etrieval
S
ystem, SRS, developed at
the EBI.
2.3
The range of applications
There is a historical bias towards sequence analysis but a wide variety of areas are now
catered for in the EMBOSS suite. There are applications for local, global and multiple
sequence alignments and tools for generating and scanning various types of profile
including hidden Markov models, thanks to the integration of Sean Eddy's HMMER
package. Tools for motif identification in protein and nucleotide sequences are also
provided. A variety of other tasks including manipulation and display of feature tables,
graphical output, database indexing and other administrative tools are also catered for.
Recently, software has been added for proteomics and protein structure. Included
are tools for identifying sequence fragments of a specified molecular weight and software
for parsing and processing the PDB, SCOP and CATH databases.
2.4
The software
EMBOSS programs are written in the computer programming language “C” and can,
currently, only be run under the UNIX operating system. To run the programs without a
GUI require that program names, together with any parameter requirements, are typed in
response to a UNIX prompt forming a command line. PCs running Windows and
Macintoshes can be used as terminals to connect to a UNIX machine offering the EMBOSS
package.
2.5
Maintenance and Support
EMBOSS is maintained by a collection of individuals, most of whom are based at the
RFCGR. They use a central repository of code that is managed by CVS (Central Version
System). EMBOSS is under very active development and the number of applications has
almost doubled in the last 18 months. To ensure quality and stability, access to the
repository is restricted to a core of active developers. Those who would like to join this
team and get full write access to the repository are encouraged to follow the “Developing
Code
and
EMBOSS
internals”
link
on
the
EMBOSS
home
page
at
http://emboss.sourceforge.net
While the developers do not promise that EMBOSS is absolutely bug free, they do
perform nightly compilation checks for the whole of EMBOSS on a variety of platforms
and, as part of their quality assurance exercise, run each application on a test data set to
ensure everything is working as anticipated.
User support, training and a means for feedback are provided via mailing lists and
regular training courses. Details can be found from the EMBOSS homepage.
