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/.

Figure 1

(A) Input form for generating signal occurrence profiles with the program OProf. Sequences around annotated translation start sites from two bacterial genomes (left side) are searched for the hexanucleotide sequence motif AGGAGG (right side) complementary to the 3′ end of 16 s ribosomal RNA. Note that the signal is searched in a sliding window of 10 bp and that one mismatch is allowed for determining its local frequency. This analysis serves to compare the strength and location of the Shine-Dalgarno mRNA–rRNA interaction motif in Escherichia coli and Bacillus subtilis in a qualitative manner. (B) Result: note that the Shine-Dalgarno interaction motif is stronger in B.subtilis than in E.coli and centered about two bases further upstream in the former species. More than a hundred bacterial genomes are now available to perform this type of analysis.