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 SSA Tools OProf: Generation of a signal occurrence profile around genomic anchor points or functional sites. The occurrence profile measures the frequency of a given motif relative to functional sites. Motifs are defined via either a position weight matrix (PWM) or a consensus sequence. Cpr: Generation of a Constraint Profile. The program identifies non-random sequence regions (without explicitly defining their context) in the neighborhood of defined functional sites. SList: Generation of a Signal List. The program detects consensus sequence-based motifs that are over- or under-represented in particular regions relative to a functional site. Motifs are defined by consensus sequences (including Ns, and mismatches). PatOp: Optimization of a Locally Over-Represented Sequence Motif. The program optimizes an initial locally over-represented sequence motif by iterative alignment. It outputs an optimized position weight matrix (PWM), including an optimized cut-off. The maximization criteria are based on local over-representation, and flanking nucleotides. FindM: Find Motifs around Functional Sites. The program locates motifs near functional sites, or select functional sites flanked by motifs. It returns a list of motif locations. FromFPS: Sequence Extraction Tool. The program extracts a set of fixed-length DNA sequences located around functional sites.

It is important to note that SSA programs serve to characterize sequence motifs that occur at constrained distances from functional genomic loci.

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