SSA (Signal Search Analysis) is a software package for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site (e.g. a transcription or translation initiation site). The SSA server provides access to four different computer programs as well as to a large number of precompiled functional site collections.

The four main programs offered by the package allow (i) the identification of non-random sequence regions under evolutionary constraint (Cpr), (ii) the detection of consensus sequence-based motifs that are over- or under-represented at a particular distance from a functional site (SList), the analysis of the positional distribution of a consensus sequence- or weight matrix-based sequence motif around a functional site (OProf), and (iv) the optimization of a weight matrix description of a locally over-represented sequence motif (PatOp).

The program FindM allows to retrieve nucleotide sequences around functional sites that may or may not contain given motifs defined by a consensus sequence or a weight matrix, whereas the FromFPS utility can be used to retrieve DNA sequence stretches of a given length that are aligned with a functional site.