BIOINFORMATICS APPLICATIONS NOTE Vol. 17 no. 6 2001Pages 577–578
SeWeR: a customizable and integrated dynamicHTML interface to bioinformatics servicesMalay 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
ABSTRACTSummary: Sequence analysis using Web Resources(SeWeR) is an integrated, Dynamic HTML (DHTML) inter-face to commonly used bioinformatics services availableon the World Wide Web. It is highly customizable, extend-able, platform neutral, completely server-independent andcan be hosted as a web page as well as being used asstand-alone software running within a web browser.Availability: The web version of SeWeR can be freelyaccessed from http://www.bioinformatics.org/sewer/ orhttp://iubio.bio.indiana.edu/webapps/SeWeR/, and alsofrom several mirror sites all over the world (a full listingis available on the SeWeR web page). It can also bedownloaded under GNU General Public License fromftp://iubio.bio.indiana.edu/molbio/analyze/sewer.zip.Contact: [email protected]
The plethora of bioinformatics services available on theWorld Wide Web necessitates the integration of these ser-vices in a seamless interface. Three such freely availableinterfaces are Baylor College of Medicine (BCM) searchlauncher (http://dot.imgen.bcm.tmc.edu:9331/; Smith etal., 1996), ORBIT (Bellgard et al., 1999) and The BiologyWorkbench (http://workbench.sdsc.edu/; Subramaniam,1998). But each of these approaches is either greatlydependent on server-side processing of data or requiresinstallation of software environments like Perl or Java.On one hand, dependency on server-side processing ofdata makes software like this difficult to port to anotherserver architecture. On the other hand, installation of asoftware environment and compilation of source code tocustomize or to extend particular software is beyond thecapabilities of casual users, and therefore, restrict the useof such services to experts.
Sequence analysis using Web Resources (SeWeR) is aversatile software that addresses all the above-mentionedlimitations. SeWeR is implemented to make use of theubiquitous presence of a new generation of web-browsersthat are amenable to programming in JavaScript. Togetherwith Cascading Style Sheets (CSS; see http://www.w3c.org/), a set of document-formatting rules, JavaScript canbe 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 independentof any additional software environment like Perl or Java.A browser is enough to run a DHTML application, whichis considerably faster than Java applets. The choice ofDHTML also enables SeWeR to transparently access theexisting service without any change of the existing serverarchitecture of a particular service. SeWeR does all itscomputation on the client browser making it capableof running as a stand-alone application from within thebrowser. Use of DHTML also makes SeWeR capable ofbeing hosted from a web site.
SeWeR presents an integrated uniform interface tocommonly used services in bioinformatics, such asnucleic acid and protein sequence retrieval and analysis,PCR related analysis, sequence alignment, databasesearching, protein structure prediction, sequence formatconversion, sequence assembly, etc. (see SeWeR web sitefor details). It also supplies all the advanced options of aparticular service. Certain common tasks like retrieving asequence from a database or a PubMed search are quicklyperformed from the top navigation panel.
A typical search page is shown in Figure 1 (in this case‘Database Searches’). All the services can be accessedthrough a common query form. The form provides accessto the help page of the selected service and also theadvanced options of the selected service. The user, aftercompleting the option form, can also customize the formby clicking on the ‘customize’ button, which opens upa new window with a form dynamically generated withall the chosen options already filled in. This customizedpage can be saved locally. The user does not need tofill in the options of a customized page. If a remoteservice is not already supported by SeWeR, the usercan incorporate the service in SeWeR in ‘Customiza-tion section’. The user has to supply the HTML pageof the service, SeWeR target page and some simpleinformation such as the URL of the service, help-pageURL, program name etc. SeWeR intelligently parses theHTML page and seamlessly incorporates the service inSeWeR.
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Fig. 1. Screen dump showing the option menu. The program chosen is BLAST.
SeWeR also provides a set of simple sequence manipu-lation tools locally. At present, the implemented tools area program to inverse-complement and another to ‘clean’a DNA sequence. The latter is a script written to getrid of number, line-breaks, spaces and other charactersfrom the sequence. A special feature of SeWeR is theuse of Bookmarklets (see http://developer.netscape.com/docs/manuals/communicator/jsguide/misc.htm). Theseare small JavaScript codes that can be executed from apersonal toolbar that can be very useful. Although usedquite often in web development, these codes were rarelyused in bioinformatics. At present the only web site inbioinformatics where bookmarklets are used is EBI SRSserver (Zdobnov et al., 2000). SeWeR offers two book-marklets as prototypes. One for the retrieving sequencefrom GeneBank and the other one for PubMed query.
In conclusion, SeWeR is a prototype interface writtenentirely in JavaScript that is cross-platform, extendable,customizable and easy to use. It provides several levels ofcustomization of the interface according to the user skill-levels and his needs. The structure of SeWeR is highlyamenable for batch processing and automation and allowsthe most efficient use of web-based sequence analysis.
ACKNOWLEDGEMENTSI gratefully acknowledge facilities provided by CCMB. Iam grateful to Dr Don Gilbert, Indiana University for hiscareful insight and critical comments on the manuscriptand also for nurturing SeWeR. I thank Dr Malay K. Ray,Dr S. Shivaji, members of Bioinformatics.org, Uma andPowrnima. I was recipient of CSIR fellowship for my PhDduring the development of SeWeR.
REFERENCESBellgard,M.I., Hiew,H.L., Hunter,A. and Wiebrands,M. (1999) OR-
BIT: an integrated environment for user-customized bioinformat-ics tools. Bioinformatics, 15, 847–851.
Goodman,D. (1998) Dynamic HTML, the Definitive Reference.O’Reilly.
Smith,R.F., Wiese,B.A., Wojzynski,M.K., Davison,D.B. and Wor-ley,K.C. (1996) BCM search launcher—an integrated interfaceto molecular biology data base search and analysis services avail-able on the World Wide Web. Genome Res., 6, 454–462.
Subramaniam,S (1998) The biology workbench—a seamlessdatabase and analysis environment for the biologist. Proteins, 32,1–2.
Zdobnov,E.M., Lopez,R., Apweiler,R. and Etzold,T. (2000) TheEBI SRS server—recent developments. Proceedings of theGerman Conference on Bioinformatics, pp. 139–147.
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