probeCheck -- a central resource for evaluating oligonucleotide probe coverage and specificity
What you can do:
Evaluate probe and primer specificity.
Highlights:
- Currently, 24 widely used sequence collections including the Ribosomal Database Project (RDP) II, Greengenes, SILVA and the Functional Gene Pipeline/Repository can be queried.
- For this purpose, probeCheck integrates a new online version of the popular ARB probe match tool with free energy (DeltaG) calculations for each perfectly matched and mismatched probe-target hybrid, allowing assessment of the theoretical binding stabilities of oligo-target and non-target hybrids.
- For each output sequence, the accession number, the GenBank taxonomy and a link to the respective entry at GenBank, EMBL and, if applicable, the query database are displayed.
- Filtering options allow customizing results on the output page.
- In addition, probeCheck is linked with probe match tools of RDP II and Greengenes, NCBI blast, the Oligonucleotide Properties Calculator, the two-state folding tool of the DINAMelt server and the rRNA-targeted probe database probeBase.
- Taken together, these features provide a multifunctional platform with maximal flexibility for the user in the choice of databases and options for the evaluation of published and newly developed probes and primers.
Keywords:
- Oligonucleotide Probes
- probe specificity
- primer specificity
Literature & Tutorials:
This record last updated: 11-24-2008