Information Technology Reference
In-Depth Information
3.2
EMBOSS GUIs
Using the UNIX command line can be daunting for many research biologists. In an attempt
to make the programs more accessible to users not familiar with command line UNIX,
several intuitive GUIs have been developed for EMBOSS. Some of these GUIs are web
based and require data to be cut and pasted into appropriate fields. Other interfaces operate
more closely with the programs of the package and can thus access data files more directly
W2H (
http://gcg.rfcgr.mrc.ac.uk/cgi-bin/w2h-emboss/w2h.start)
Of the many web pages that have been designed as an interface for EMBOSS, this is
possibly the most comprehensive. It allows upload of files from RFCGR and local disk,
together with a minimal file management system. There is a simple interface and an
advanced one for the more experienced user. Files and applications are accessed by double
clicking on the relevant buttons, and each time a piece of information is requested, a new
browser window opens. Operation of the site is not always obvious, and if Java is available
on your computer, then you might be advised to spend the induction time on Jemboss
instead.
PBI (
http://bioinfo.pbi.nrc.ca:8090/EMBOSS/index.html)
An easy web site to use, this was developed at the Plant Biotechnology Institute in
Canada. The basic site is not connected to any file management system, and is simply a
means of running the EMBOSS applications on your data. Simply choose the relevant
application, cut and past the data, and run. The results will appear in the same browser
window. The web pages for this site can be downloaded and installed locally. The
installation is very simple.
SPIN (
http://staden.sourceforge.net)
SPIN is the program in the Staden package that offers sequence analysis tools. In
common with other Staden package programs, it allows third party software to be accessed
from its Graphical Interface. In particular, the whole of the EMBOSS package can be
accessed from behind the SPIN interface. The Graphical Interface of SPIN, although not
fully developed, is currently superior to any other EMBOSS GUI. In particular, SPIN offers
graphical outputs that are interactive (i.e. it is possible to invoke information from a
graphical output by clicking on features) and can be customised and combined freely. The
Staden package is now open source and both source code and binaries for Windows, UNIX
and MacOS X are freely available from the Staden package sourceforge home page. The
only caveat to using SPIN is that it is currently not actively supported which means that
integration of EMBOSS is limited to Version 2.8.0.
3.2.4 Jemboss (http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/)
Jemboss [2,3] is the new interface written for EMBOSS at the RFCGR. It is written in the
programming language Java primarily to enable it to run on almost any computer (in
particular, Java for MacOS and earlier versions will not run Jemboss, although Jemboss
will run under MacOS X). It is designed as a “point and click” interface and offers an easy
route to sequence analysis for the biological researcher. Jemboss was written primarily as
