title: Signal search analysis server.
abstract: 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/.
authors.affiliation: ISREC Swiss Institute for Experimental Cancer Research, Ch. des Boveresses 155, 1066 Epalinges s/ Lausanne, VD, Switzerland.
authors.forename: Giovanna
authors.initials: G
authors.lastname: Ambrosini
authors.forename: Viviane
authors.initials: V
authors.lastname: Praz
authors.forename: Vidhya
authors.initials: V
authors.lastname: Jagannathan
authors.forename: Philipp
authors.initials: P
authors.lastname: Bucher
mesh_terms: D016384:Consensus Sequence; D016680:Genome, Bacterial; D020407:Internet; D011401:Promoter Regions, Genetic; D014176:Protein Biosynthesis; D012336:RNA, Ribosomal, 16S / Q000737:chemistry; D012045:Regulatory Sequences, Nucleic Acid; D020218:Response Elements; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D024363:Transcription Initiation Site
chemical_list: D012336:RNA, Ribosomal, 16S