(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
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.
Generation of a Constraint Profile.
The program identifies non-random sequence regions (without explictly defining their context) in the neighborhood of defined funtional sites.
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).
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.
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.
Sequence Extraction Tool.
The programm 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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