Description: SynaProbe™ enables whole genome/transcriptome screening of SARS microarray probe candidates within milliseconds.
Application Example: In a stepwise approach to rational probe design, MGRC SynaProbe Design and Hybridization were used to determine subtype specific probes for the SARS Coronavirus. Probes targets were deduced from whole genome viral alignments with SynaBASE and subsequently designed and hybridized, respectively. Results show specific matches to the target SARS virus and SynaProbe Hybridization confirms probes determined by previous methods.
To try SynaProbe Design, please:

1. Click here and then click on the “Access Now” button
2. Click on SynaProbe Design and make sure the query type is set to Nucleotide-nucleotide.
3. Click on the ‘test sequence’ button and get the SARS Target sequence fragment into the ‘Sequence’ box by clicking on the ‘Copy’ button.
4. The ‘Viral genomes’ SynaBASE should be selected.
5. Select 50 as the probe sequence length
6. Using the default parameters, click on ‘PROBE DESIGN’ to begin your analysis.
7. Once you have your results in a probe location graph, you can manipulate the graph by adjusting the weighting parameters. Select 5.0 and 3.0 for Uniqueness and Position weightings, respectively. Probes shall be redesigned and displayed in real time.
8. Highlight probe candidate number 1 and click the button to link directly to Synaprobe Hybridization.
9. To perform any other type of analysis such as mining for functional and structural annotations with the buttons on the right.
Align SARS to All viral genomes in SynaBASE
- SynaSearch: 1 second
Design candidate probes using conserved regions found in previous alignments against all Genbank viral genomes
- SynaProbe: 128 milliseconds
Confirm probe specificity by searching all viral Genomes allowing up to 10 mismatches
- SynaProbe Hybridization: 29 milliseconds/probe