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Nucleic Acids Research, 2003, Vol. 31, No. 13 3618-3620
© 2003 Oxford University Press

Signal search analysis server

Giovanna Ambrosini1, Viviane Praz1,2, Vidhya Jagannathan1 and Philipp Bucher*,1,2

1 ISREC Swiss Institute for Experimental Cancer Research, Ch. des Boveresses 155, 1066 Epalinges s/ Lausanne, VD, Switzerland 2 SIB Swiss Institute of Bioinformatics, Ch. des Boveresses 155, 1066 Epalinges s/ Lausanne, VD, Switzerland

*To whom correspondence should be addressed at ISREC Swiss Institute for Experimental Cancer Research, Ch. des Boveresses 155, 1066 Epalinges s/ Lausanne, VD, Switzerland. Tel: +41 21 692 5892; Fax: +41 21 653 4768; Email: phillipp.bucher{at}isrec.unil.ch

Signal search analysis is a general method to discover and characterize sequence motifs that are positionally correlated with a functional site (e.g. a transcription or translation start site). The method has played an instrumental role in the analysis of eukaryotic promoter elements. The signal search analysis server provides access to four different computer programs as well as to a large number of precompiled functional site collections. The programs offered allow: (i) the identification of non-random sequence regions under evolutionary constraint; (ii) the detection of consensus sequence-based motifs that are over- or under-represented at a particular distance from a functional site; (iii) the analysis of the positional distribution of a consensus sequence- or weight matrix-based sequence motif around a functional site; and (iv) the optimization of a weight matrix description of a locally over-represented sequence motif. These programs can be accessed at: http://www.isrec.isb-sib.ch/ssa/.


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