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Prider – multiplexed primer design using linearly scaling approximation of set coverage

View ORCID ProfileNiina Smolander, View ORCID ProfileManu Tamminen
doi: https://doi.org/10.1101/2021.09.06.459073
Niina Smolander
1Department of Biology, University of Turku, Turku, Finland
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Manu Tamminen
1Department of Biology, University of Turku, Turku, Finland
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  • For correspondence: manu.tamminen@utu.fi
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Abstract

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 primers and probes to complex, heterogeneous DNA data sets, an optimization problem arises 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.

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 reduced by removing components of high redundancy or narrow coverage. The primers from the resulting near-optimal coverage are easily accessible as data frames and their coverage across the input sequences can be visualized as heatmaps using Prider’s plotting function. Prider scales linearly to increasing sequence data and therefore permits efficient design of primers to large and highly diverse DNA datasets.

Prider is available on GitHub under the permissive BSD-3-clause license:

https://github.com/manutamminen/prider

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://zenodo.org/record/5361309

  • https://github.com/manutamminen/prider

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 06, 2021.
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Prider – multiplexed primer design using linearly scaling approximation of set coverage
Niina Smolander, Manu Tamminen
bioRxiv 2021.09.06.459073; doi: https://doi.org/10.1101/2021.09.06.459073
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Prider – multiplexed primer design using linearly scaling approximation of set coverage
Niina Smolander, Manu Tamminen
bioRxiv 2021.09.06.459073; doi: https://doi.org/10.1101/2021.09.06.459073

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