SynaRex™ is an application that can be used for finding motifs or patterns defined by a regular expression. It is built upon the SynaBASE™ structured network database platform 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 human translationally controlled tumor protein (TCTP, P13693) was found to be expressed in human mammary carcinoma cells. It shares the translationally controlled tumour protein signature 1 (PROSITE ID TCTP_1) with 61 other proteins. Each of these proteins has a domain with a pattern represented by the regular expression [IFAED]-[GA]-[GASF]-N-[PAK]-S-[GTA]-E-[GDEVCF]-[PAGEQV]-[DEQGAV]. As protein databases grow, searching known patterns quickly and easily is crucial to finding novel candidates. To address this issue, SynaRex offers a simple web-based searching method for rapidly identifying motifs. By using PROSITE regular expressions as the input query, proteins with the TCTP_1 signature can be rapidly identified. By searching UniProtKB/Swiss-Prot Release 52.1, SynaRex identifies all 62 protein sequences that fit the regular expression defined above. These sequences can be further categorized into 37 distinct patterns (Figure 2). The protein sequence for P13693, together with 7 other mammalian and avian protein sequences has the pattern IGGNASAEGPE (Figure 3). Grouping the sequences into patterns assists further refinement of the understanding of protein function because proteins with diverged structures and overall functions may still have strong evolutionary pressure to conserve important domains. When compared to sequential search tools such as Fuzzpro (EMBOSS 4.1.0), under comparable environments, SynaRex reports results 400-fold faster with similar sensitivity.
To run the example above, please:
  1. Go to
  2. Click on SynaREX.
  3. Select 'Protein' for Query Type.
  4. Click on Test Sequence.
  5. Select the Application Note test sequence - May 2007 by clicking on Copy next to the sequence.
  6. Select the 'UniProtKB/Swiss-Prot Release 52.1' SynaBASE and leave all other parameters at default.
  7. Click on FIND Sequence to begin your analysis.
Figure 1:The query submission page of SynaRex (2.1.1).
Figure 2:SynaRex results page showing the 62 times the pattern occurred on the forward direction and the 37 specific patterns that it can be grouped into.
Figure 3:SynaRex results page that shows the group of 8 sequences with the pattern IGGNASAEGPE of which P13693 is a member.

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