Description: SynaRex™ (v. 2.1.0) is an application used for finding motifs or patterns defined by a regular expression. It is built upon the SynaBASE structured network database architecture which results in enhanced sensitivity and performance. It reports the position of the pattern, the sequence and the matching regular expression in gff format.
Application Example: The recognition site of Human Interferon (IFN) regulatory factor 2 (IRF-2) can be represented by the regular expression [CGT][AG]A[AT]A[AG][CT]GAAA[CG][CGT]X[AGT]XXX, as given in the profile for MA0051 (JASPAR). Recognition sites such as these are usually derived from common sequences at promoter regions linked to the gene being studied. However, questions often arise regarding the specificity of the recognition site, the number of such sites present in the genome, or the possibilities of the existence of genes that are co-regulated by transcription factors. To address these questions, SynaREX offers a simple web-based searching method for identifying motifs. By using PROSITE regular expressions as the input query, candidate IRF-2 recognition sites on the Human Genome can be readily identified. Compared to sequential search tools such as Fuzznuc (EMBOSS 4.0.0), SynaRex is 300 fold faster and identifies over 16,000 putative sites.
To run the example above, please:
  1. Click here.
  2. Click on “SynaRex”.
  3. Click on the ''test sequence'' and use the Newsbyte test sequence labelled 'Human Interferon (IFN) regulatory factor 2 (IRF-2) (JASPAR MA0051)' by clicking on the 'Copy' button next to the sequence.
  4. Select the 'Homo sapiens genome (NCBI Build 36 v1)' SynaBASE.
  5. Set Logo Max Hits and Report Max Hits reference to 50,000.
  6. Using the default parameters given, click on 'Find Sequence' to begin your analysis.
Figure 1: The query submission page of SynaRex (2.1.0).
Figure 2: SynaRex results page showing the 12,613 patterns and 16,632 occurrences that fit the IRF-2 recognition site and their frequency.

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