Most web interfaces provide a form for setting options and running applications. To use a web interface, all you need are a web browser and Internet access. Some sites allow anonymous access, but in most cases you will be expected to register with the site before you can use their services.
Difficulties can arise in generating an interface because of dependencies in the application ACD files. These include cases where the value of one parameter depends on the value or property of another, for example sequence length, or where the available options depend on the input, for example whether a sequence is DNA or protein. Some web interfaces handle dependencies better than others.
The available web interfaces include
wEMBOSS is a popular and powerful web interface. If features:
Results from program runs remain stored permanently on the server.
Personal workspace and project folders (nested at any depth) help to manage rationally data and results.
Each program has a panel with dynamic hiding/unhiding of available options.
On-line access to program manuals and a program search facility
The site administrator can exclude EMBOSS programs from wEMBOSS.
Some program outputs can be automatically opened with applets or plug-ins.
WebLab is a multifunctional bioinformatics analysis platform integrating diverse tools with a unified, user-friendly web interface. WebLab includes data management functions, group strategy and knowledge sharing mechanisms for the biomedical scientist.
http://embossgui.sourceforge.net/
EMBOSS Explorer is a very popular web-based graphical user interface. It is extremely simple to install, configure, maintain and use.
http://www.w2h.dkfz-heidelberg.de/
W2H is a free WWW interface to EMBOSS and other sequence analysis software including the GCG-Package (Genetic Computer Group) and derived services (such as HUSAR, Heidelberg Unix Sequence Analysis Resources). It tries to cover as much functionality and be as user-friendly as possible. It includes more than one hundred programs and runs on any computer platform with a JavaScript enabled web browser.
SRS is the most widely used biological database indexing and query system worldwide. In addition to the database query capabilities, SRS includes external application definitions written in the Icarus language. The EMBOSS developers and Lion Bioscience collaborated to develop Icarus definitions for many of the EMBOSS applications which are now maintained by EMBL-EBI.
BioManager provides a single, user-friendly, and intuitive web interface to EMBOSS and a number of other freeware analysis programs, as well as the major genetic databases. It is available through subscription.
http://www.bioinfo.de/isb/WEB01/bruno.html
BioNavigator is a web-based platform for sequence and structure analysis that integrates a applications and databases under a streamlined, intuitive user interface. BioNavigator was designed for research but also for the practical teaching of sequence analysis, with a broad range of industry-standard applications accessible from multiple locations without the need to install specialized software. BioNavigator's standardized interface enables students to concentrate on using programs rather than wasting time learning how to navigate each program's interface.
http://soaplab.sourceforge.net/soaplab2/SpinetClient.html
Spinet is a basic web interface for Soaplab Web Services which can be used to run EMBOSS programs through web forms.