BIOINFORMATICS APPLICATIONS NOTE Vol. 17 no. 6 2001 Pages 577–578 SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services Malay Kumar Basu Centre for Cellular and Molecular Biology, Hyderabad 500007, India Received on August 25, 2000; revised on January 30, 2001; accepted on March 2, 2001 ABSTRACT Summary: Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) inter- face to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extend- able, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. Availability: The web version of SeWeR can be freely accessed from http://www.bioinformatics.org/sewer/ or http://iubio.bio.indiana.edu/webapps/SeWeR/, and also from several mirror sites all over the world (a full listing is available on the SeWeR web page). It can also be downloaded under GNU General Public License from ftp://iubio.bio.indiana.edu/molbio/analyze/sewer.zip. Contact: [email protected] The plethora of bioinformatics services available on the World Wide Web necessitates the integration of these ser- vices in a seamless interface. Three such freely available interfaces are Baylor College of Medicine (BCM) search launcher (http://dot.imgen.bcm.tmc.edu:9331/; Smith et al., 1996), ORBIT (Bellgard et al., 1999) and The Biology Workbench (http://workbench.sdsc.edu/; Subramaniam, 1998). But each of these approaches is either greatly dependent on server-side processing of data or requires installation of software environments like Perl or Java. On one hand, dependency on server-side processing of data makes software like this difficult to port to another server architecture. On the other hand, installation of a software environment and compilation of source code to customize or to extend particular software is beyond the capabilities of casual users, and therefore, restrict the use of such services to experts. Sequence analysis using Web Resources (SeWeR) is a versatile software that addresses all the above-mentioned limitations. SeWeR is implemented to make use of the ubiquitous presence of a new generation of web-browsers that are amenable to programming in JavaScript. Together with Cascading Style Sheets (CSS; see http://www.w3c. org/), a set of document-formatting rules, JavaScript can be used to generate sophisticated user interfaces and can turn a static HTML page into a truly interactive web- application. Dynamic HTML (DHTML; Goodman, 1998) has the added advantage of being completely independent of any additional software environment like Perl or Java. A browser is enough to run a DHTML application, which is considerably faster than Java applets. The choice of DHTML also enables SeWeR to transparently access the existing service without any change of the existing server architecture of a particular service. SeWeR does all its computation on the client browser making it capable of running as a stand-alone application from within the browser. Use of DHTML also makes SeWeR capable of being hosted from a web site. SeWeR presents an integrated uniform interface to commonly used services in bioinformatics, such as nucleic acid and protein sequence retrieval and analysis, PCR related analysis, sequence alignment, database searching, protein structure prediction, sequence format conversion, sequence assembly, etc. (see SeWeR web site for details). It also supplies all the advanced options of a particular service. Certain common tasks like retrieving a sequence from a database or a PubMed search are quickly performed from the top navigation panel. A typical search page is shown in Figure 1 (in this case ‘Database Searches’). All the services can be accessed through a common query form. The form provides access to the help page of the selected service and also the advanced options of the selected service. The user, after completing the option form, can also customize the form by clicking on the ‘customize’ button, which opens up a new window with a form dynamically generated with all the chosen options already filled in. This customized page can be saved locally. The user does not need to fill in the options of a customized page. If a remote service is not already supported by SeWeR, the user can incorporate the service in SeWeR in ‘Customiza- tion section’. The user has to supply the HTML page of the service, SeWeR target page and some simple information such as the URL of the service, help-page URL, program name etc. SeWeR intelligently parses the HTML page and seamlessly incorporates the service in SeWeR. c Oxford University Press 2001 577 Downloaded from https://academic.oup.com/bioinformatics/article/17/6/577/272399 by guest on 03 January 2022