Oligo Design Links
We have created the following resources for design and analysis of oligonucleotide probes and primers:
For detection of chimeras in 16S rRNA sequences:
- DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Download the paper here
For Fluorescence In Situ Hybridization:
- MathFISH, an online resource for the evaluation of rRNA-targeted FISH probes. Download the paper here
- Design Probes, a tool in the DECIPHER package to design optimal FISH probes for targeting one group of RNA sequences in the presence of many non-target groups. See abstract here.
- ProbeMelt, a tool in DECIPHER to determine hybridization efficiencies at different formamide concentrations
- 16S Oligos, a database of genus specific FISH probes pre-designed with the Design Probes tool. In provides information on specificity and coverage for each probe, and offers additional specificity with the dual probe option, in which true identifications are based on the overlap of two separate probes. See abstract here
For PCR:
- Design Primers, a tool in the DECIPHER package to design the optimal set of PCR primers for targeting one group of DNA sequences in the presence of many non-target groups. It can take advantage of the effect of 3′-end mismatches in elongation efficiency. See abstract here
- 16S Oligos, a database of genus specific primers pre-designed with the Design Primers tool. In provides information on specificity and coverage for each primer set. See abstract here
For Microarrays:
- Design Array, a tool in the DECIPHER package to create the optimal set of probes for distinguishing many groups of DNA sequences using a microarray. Download the paper here
- The Design Array tool makes use of the ProbeMelt model to design probes with optimal sensitivity and specificity for each target group of sequences