EMBnet is a consortium of collaborating bioinformatics groups located mainly within Europe (http://www.embnet.org). Each member country is represented by a ‘node', a group responsible for the maintenance of local services for their users (e.g. education, training, software, database distribution, technical support, helpdesk). Among these services a web portal with links and access to locally developed and maintained software is essential and different for each node. Our web portal targets biomedical scientists in Switzerland and elsewhere, offering them access to a collection of important sequence analysis tools mirrored from other sites or developed locally. We describe here the Swiss EMBnet node web site (http://www.ch.embnet.org), which presents a number of original services not available anywhere els

Bordoli, Lorenza

Falquet, Laurent

Ioannidis, Vassilios

Jongeneel, C. Victor

Pagni, Marco

RERO DOC Digital Library

Swiss EMBnet node web serverLaurent Falquet*, Lorenza Bordoli1, Vassilios Ioannidis, Marco Pagni andC. Victor Jongeneel2Swiss Institute of Bioinformatics (SIB), CH-1066 Epalinges, Lausanne, Switzerland, 1Swiss Institute ofBioinformatics (SIB), Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland and2Swiss Institute of Bioinformatics (SIB) and Ofﬁce of Information Technology, Ludwig Institute for Cancer Research,CH-1066 Epalinges, Lausanne, SwitzerlandReceived February 17, 2003; Revised and Accepted March 25, 2003ABSTRACTEMBnet is a consortium of collaborating bioinfor-matics groups located mainly within Europe (http://www.embnet.org). Each member country is repre-sented by a ‘node’, a group responsible for themaintenance of local services for their users (e.g.education, training, software, database distribution,technical support, helpdesk). Among these servicesa web portal with links and access to locallydeveloped and maintained software is essentialand different for each node. Our web portal targetsbiomedical scientists in Switzerland and elsewhere,offering them access to a collection of importantsequence analysis tools mirrored from other sites ordeveloped locally. We describe here the SwissEMBnet node web site (http://www.ch.embnet.org),which presents a number of original services notavailable anywhere else.BACKGROUNDThe EMBnet organization, founded in 1988, regroups 32country nodes and seven special nodes in 2003. EMBnetcreated the first gopher and World Wide Web servers in biology(CSC BioBox http://www.csc.fi/molbio). EMBnet developed,among others, solutions for daily database updates using theinternet (NDT), distributed computing (HASSLE) and efficientdatabase browsing and linking (SRS) (1). EMBnet is committedto bringing the latest software algorithms to users worldwidefree of charge and continues to develop state-of-the-art publicdomain software (EMBOSS) (2). Many bioinformatics coursesat different levels and covering multiple topics are organizedevery year by EMBnet nodes in various countries.Altogether, the nodes reach a user base of tens of thousandsof scientists around the world and provide them with mirrors ofup-to-date databases (e.g. EMBL, SWISS-PROT, TrEMBL,PROSITE, InterPro, ENSEMBL) and software, among whichmany are only accessible on a particular node web site.THE Swiss EMBnet WEB SITEThe Swiss EMBnet node was created by Reinhard Do¨lz in1988 at the Biozentrum in Basel and in 1997 moved to theSIB (Swiss Institute of Bioinformatics, http://www.isb-sib.ch)under the responsibility of Victor Jongeneel and AmosBairoch. The Swiss EMBnet node currently employs threepersons (two full-time positions) funded by a grant from theSwiss government. The services offered through the SwissEMBnet web site are divided into several categories, e.g.sequence searches in databases, protein function prediction,dotplots, pairwise and multiple alignments, coding regionprediction, and tools for the exploration of protein motifsand domains. The Swiss EMBnet node server receives>2300 daily requests for pages, from *.com (18%), *.edu(13%), *.net (7.5%), *.uk (5%), *.ch (4.5%), *.de (4%),*.org (3%), *.fr (2.5%), other (20%), unresolved (22%). Userfeedback has generally been very positive and the staff aimto respond to suggestions and requests for services ordocuments.CONTENT OF THE CURRENT WEB SITEThe latest update of the web site (January 2003) provides thefollowing software tools: (an asterisk indicates that the SwissEMBnet node web server is an exclusive repository site for thesoftware or provides a unique implementation of the software).Computer programs*BLAST (basic and advanced). Local implementation of theNCBI BLAST2 with many options and databases not seen onother BLAST servers. The output is slightly reformatted to addlinks to external databases and to display a graphical viewof the matches based on a Perl script kindly provided byDr Alessandro Guffanti (3).FDF. An access to our local GeneMatcherTM (http://www.paracel.com) for fast protein sequence searches using ahardware-implemented version of the Smith–Waterman algo-rithm. The input forms and output parser are almost identicalto those used on the BLAST pages.Nucleic Acids Research, Vol. 31, No. 13 # Oxford University Press 2003; all rights reserved*To whom correspondence should be addressed. Tel: þ41 216925954; Fax: þ41 216925945; Email: laurent.falquet@isb-sib.ch3782–3783 Nucleic Acids Research, 2003, Vol. 31, No. 13DOI: 10.1093/nar/gkg547PRSS3. To evaluate the statistical significance of a pairwiseprotein sequence alignment (4–6).LALIGN. To calculate a local or global pairwise alignmentbetween two sequences (part of the FASTA package) (7).ClustalW. ClustalW multiple sequence alignment software (8).T-Coffee. T-Coffee multiple sequence alignment software (9).BOXSHADE. Multiple alignment coloring and formattingtool for publication.EMBOSS. The Pise interface to the EMBOSS package (2,10).*Fetch. A simple tool to retrieve sequences from locallymaintained databases.*HITS. A local database and many tools devoted to analyz-ing protein domains and motifs, developed at SIB (11).*PFSCAN. A local tool to scan protein sequences for matcheswith PROSITE patterns profiles and Pfam HMMs (12).*PFRAMESCAN. A local tool to scan short DNA sequences(translated on-the-fly into protein) for possible matches withPROSITE profiles (12), allowing for frame-shift errors in theDNA sequence.PatternFind. A local pattern search tool, allowing the user toenter his/her own pattern and search protein databases forpotential matches (12).*Dotlet. A Java applet to visualize and tune dot plots interac-tively (similar to Dotter) developed at the SIB (13).*iPCR. Virtual PCR product extractor developed at the SIB.*ESTScan2. A tool to detect coding regions in EST-typecDNA sequences with the ability to correct for frame shiftsdeveloped at SIB (14).*TMPRED. A local tool to detect trans-membrane regionsand their orientation (15).*COILS. A local tool to detect possible coil-coiled regions inproteins (16).SAPS. A local tool to collect statistics about proteinssequences (17).DatabasesEPD. The Eucaryotic Promoter Database developed andmaintained at SIB (18).PROSITE. The PROSITE database developed and main-tained at SIB (12).STACK. A repository mirror of the South African STACKdatabase to increase speed downloads in Europe, requires aregistration at SANBI (19).OtherLinks to many other useful sites, ftp server with sources codeand executables of many software.FUTURE DEVELOPMENTSThe Swiss EMBnet node plans several developments of itsweb site. Among them, the implementation of a web interfacefor Marcoil, a coiled-coil detection tool using HMMs (20). Wealso plan to offer a local mirror site of the ENSEMBL project(www.ensembl.org) (21), incorporating, in addition, a differentcollection of genomes. In order to better answer our usersrequests, we are planning to install a help desk ticketing systemand to develop more documentation pages (e.g. FAQs, usermanuals). On a more general basis we are committed tomaintain and enhance the current set of installed software toolsand databases.REFERENCES1. Zdobnov,E.M., Lopez,R., Apweiler,R. and Etzold,T. (2002) The EBISRS server—new features. Bioinformatics, 18, 1149–1150.2. Rice,P., Longden,I. and Bleasby,A. (2000) EMBOSS: the EuropeanMolecular Biology Open Software Suite. Trends Genet., 16, 276–277.3. Altschul,S.F., Madden,T.L., Scha¨ffer,A.A., Zhang,J., Zhang,Z., Miller,W.and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a newgeneration of protein database search programs. Nucleic Acids Res.,25, 3389–3402.4. Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biologicalsequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444–2448.5. Pearson,W.R. (1990) Rapid and sensitive sequence comparison withFASTP and FASTA. Methods Enzymol., 183, 63–98.6. Karlin,S. and Altschul,S.F. (1990) Methods for assessing the statisticalsignificance of molecular sequence features by using general scoringschemes. Proc. Natl Acad. Sci. USA, 87, 2264–2268.7. Huang,X. and Miller,W. (1991) A time-efficient, linear-space localsimilarity algorithm. Adv. Appl. Math., 12, 337–357.8. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W:improving the sensitivity of progressive multiple sequence alignmentthrough sequence weighting, position-specific gap penalties and weightmatrix choice. Nucleic Acids Res., 22, 4673–4680.9. Notredame,C., Higgins,D. and Heringa,J. (2000) T-Coffee: a novel methodfor multiple sequence alignments. J. Mol. Biol., 302, 205–217.10. Letondal,C. (2001) A web interface generator for molecular biologyprograms in Unix. Bioinformatics, 17, 73–82.11. Pagni,M., Iseli,C., Junier,T., Falquet,L., Jongeneel,V. and Bucher,P.(2001) trEST, trGEN and Hits: access to databases of predictedprotein sequences. Nucleic Acids Res., 29, 148–151.12. Falquet,L., Pagni,M., Bucher,P., Hulo,N., Sigrist,C.J., Hofmann,K.and Bairoch,A. (2002) The PROSITE database, its status in 2002.Nucleic Acids Res., 30, 235–238.13. Junier,T. and Pagni,M. (2000) Dotlet: diagonal plots in a web browser.Bioinformatics, 16, 178–179.14. Iseli,C., Jongeneel,C.V. and Bucher,P. (1999) ESTScan: a program fordetecting, evaluating, and reconstructing potential coding regions in ESTsequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 138–148.15. Hofmann,K. and Stoffel,W. (1993) TMbase—a database of membranespanning proteins segments. Biol. Chem. Hoppe-Seyler, 374, 166.16. Lupas,A., Van Dyke,M. and Stock,J. (1991) Predicting coiled coils fromprotein sequences. Science, 252, 1162–1164.17. Brendel,V., Bucher,P., Nourbakhsh,I., Blaisdell,B.E. and Karlin,S. (1992)Methods and algorithms for statistical analysis of protein sequences.Proc. Natl Acad. Sci. USA, 89, 2002–2006.18. Praz,V., Pe´rier,R.C., Bonnard,C. and Bucher,P. (2002) The EukaryoticPromoter Database, EPD: new entry types and links to gene expressiondata. Nucleic Acids Res., 30, 322–324.19. Christoffels,A., van Gelder,A., Greyling,G., Miller,R., Hide,T. andHide,W. (2001) STACK: Sequence Tag Alignment and ConsensusKnowledgebase. Nucleic Acids Res., 29, 234–238.20. Delorenzi,M. and Speed,T. (2002) An HMM model for coiled-coil domainsand a comparison with PSSM-based predictions. Bioinformatics, 18, 617–625.21. Clamp,M., Andrews,D., Barker,D., Bevan,P., Cameron,G., Chen,Y.,Clark,L., Cox,T., Cuff,J., Curwen,V. et al. (2003) Ensembl 2002:accommodating comparative genomics. Nucleic Acids Res., 31, 38–42.Nucleic Acids Research, 2003, Vol. 31, No. 13 3783

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