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24-04-2017 -- OPROF/CPR: new Sequence Shuffling feature

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 explictly defining their context) in the neighborhood of defined funtional 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 ober-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 programm extracts a set of fixed-length DNA sequences located around functional site.

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

You find our on-line Tutorial here.

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Last update October 2017