Prider: multiplexed primer design using linearly scaling approximation of set coverage.

ABSTRACT:

Background

Designing oligonucleotide primers and probes is one of the key steps of various laboratory experiments such as multiplexed PCR or digital multiplexed ligation assays. When designing multiplexed primers and probes to complex, heterogeneous DNA data sets, an optimization problem can arise where the smallest number of oligonucleotides covering the largest diversity of the input dataset needs to be identified. Tools that provide this optimization in an efficient manner for large input data are currently lacking.

Results

Here we present Prider, an R package for designing primers and probes with a nearly optimal coverage for complex and large sequence sets. Prider initially prepares a full primer coverage of the input sequences, the complexity of which is subsequently r

SUBMITTER: Smolander N 

PROVIDER: S-EPMC9097127 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature