Primers computed by PriSeT on clades found in freshwater plankton and SARS-CoV-2 genomes.
The plankton subfolder contains a list of published primer pairs (known_primers.csv) used for comparison with PriSeT's primers, a list of at most 50 most frequent primers per clade (<taxid>_primers.csv), and mixed list with published and de novo primers ranked by frequency (<taxid>_versus_known.csv).
The file known_primers.csv contains DNA4 encoded primer pairs.
| Primer | Fwd ID | Fwd Seq | Rev ID | Rev Seq | Reference |
|---|---|---|---|---|---|
| 23S | 23S fwd | GGACARAAAGACCCTATG | A23SrVR1 | AGATCAGCCTGTTATCC$ | |
| CHLORO | ChloroF | TGGCCTATCTTGTTGGTCTGT | ChloroR | GAATCAACCTGACAAGGCAAC | |
| DIAZ | D512for | ATTCCAGCTCCAATAGCG | D978rev | GACTACGATGGTATCTAATC | |
| DIV4 | DIV4for | GCGGTAATTCCAGCTCCAATAG | DIV4rev3 | CTCTGACAATGGAATACGAATA | |
| EUK14 | F-566a | CAGCAGCCGCGGTAATTCC | R-1200 | CCCGTGTTGAGTCAAATTAAGC | |
| EUK15 | TAReuk454FWD1 | CCAGCASCYGCGGTAATTCC | TAReukREV3 | ACTTTCGTTCTTGATYRA | |
| EUKA (EA) | EUKAF | GCCGCGGTAATTCCAGCTC | EUKAR | CYTTCGYYCTTGATTRA | |
| nSSU | G18S4 | GCTTGTCTCAAAGATTAAGCC | 22R | GCCTGCTGCCTTCCTTGGA | |
| SSU | SSU556F | CGCGGTAATTCCAGCTYC | SSU911R | ATYCAAGAATTTCACCTCTGAC |
File prefix corresponds to the clade ID according to NCBI's taxonomy.
id_primers.csvcontains the top 50 de novo computed primers w.r.t. frequencyid_known_primers.csvis the result of a meta analysis that compares frequency and coverage rates with known primers (see Table above)
The file S2_Primers_PriSeT_SARS-CoV-2.csv contains 114 primer pairs and amplicons computed on 19 SARS-CoV-2 genomes. The primers produce amplicons selective for SARS-CoV-2, and have no 100 % sequence identity matches to sequences outside the Sarbecoviruses and most are even distinct from other Sarbecoviruses (e.g. bat or pangolin isolates) verified via online BLAST searches against GenBank's nr/nt dataset on 3rd of April 2020. The approximate locations are shown in the figure below. The first four digits of the de novo primer identifiers are displayed.
