Author: Marie Hoffmann; Michael T. Monaghan; Knut Reinert
Title: PriSeT: Efficient De Novo Primer Discovery Document date: 2020_4_7
ID: 3b3hv53b_6_1
Snippet: rity thresholds set high (i.e., > 97 %). Despite these natural imperfections, ecologists found that the small subunit RNA gene (SSU) is an excellent source for species-specific markers. Hence a large number of entries in the NCBI-GenBank nucleotide database originate from ribosomal subunits (Benson et al., 2012) . Schmidt et al. (2014) demonstrated that OTUs from 16S/18S rRNA reflect the underlying ecological diversity consistently across habitat.....
Document: rity thresholds set high (i.e., > 97 %). Despite these natural imperfections, ecologists found that the small subunit RNA gene (SSU) is an excellent source for species-specific markers. Hence a large number of entries in the NCBI-GenBank nucleotide database originate from ribosomal subunits (Benson et al., 2012) . Schmidt et al. (2014) demonstrated that OTUs from 16S/18S rRNA reflect the underlying ecological diversity consistently across habitats. In other words, even if OTUs cannot be resolved, their counts correlate to the sample's diversity and are roughly independent from the species composition. Finding the optimal set of primers in terms of coverage and resolution takes many costly iterations of trial and error (Elbrecht et al., 2019) . Scientists encounter problems like missing ground truth and sparsely populated reference databases. Often they would start with primer sequences published in previous studies on similar data sets and then compare OTU diversity between different primer sets. More formally, primer candidates can be described as kmers -DNA oligomers of length k -satisfying a set of sequence constraints C s which are relevant for the success of the PCR and which must hold independent of their matching. C s comprises range limits for melting temperature, CG content or low probabilities for self-annealing. When combining two k-mers to produce a primer pair, both have to fulfill a second set of constraints C p arising from their strand orientation and fitting: avoidance of CG clamps or low probability of cross-annealing.
Search related documents:
Co phrase search for related documents- data set and error trial: 1, 2
- data set and ground truth: 1, 2, 3, 4, 5, 6
- data set and large number: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39
- data set and low probability: 1
- data set and optimal set: 1, 2, 3, 4, 5, 6, 7, 8, 9
- data set and PCR success: 1
- data set and previous study: 1, 2, 3, 4, 5, 6, 7, 8, 9
- data set and primer pair: 1, 2, 3
- data set and primer sequence: 1, 2, 3
- data set and primer set: 1, 2, 3, 4, 5, 6
- data set and range limit: 1
- data set and reference database: 1, 2
- data set and resolution coverage: 1
- data set and ribosomal subunit: 1
- data set and RNA gene: 1, 2, 3, 4, 5, 6, 7
- data set and sample diversity: 1
- data set and second set: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26
- data set and self annealing: 1
- data set and sequence set: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24
Co phrase search for related documents, hyperlinks ordered by date