Tutorial/help

How to use MRPrimerV

MRPrimerV

  • Why MRPrimerV?
  • MRPrimerV is available for free and open website for searching virus specific primers instantly.

    MRPrimerV has three distinctive features:
    (i) searching top-1 primer pairs for viruses.
    (ii) suggesting the order of coding sequences for PCR experiments.
    (iii) supporting several ways to search, such as by organism, keywords, GenBank accession for genome level, and NCBI gene symbol and NCBI Gene ID for coding gene level.
    * See more details in About page.

Search primers

  • Search by
  • User may search primers by organism, keywords, GenBank accession for genome level, and NCBI gene symbol and NCBI Gene ID for coding gene level. User can find exact search terms from NCBI GenBank.

  • For text
  • The user can search only single virus name or Accession number.

    Examples

  • Organism: Zaire ebolavirus
  • Keywords: Zaire ebolavirus isolate Ebola
  • GenBank Accession number: NC_002549.1
  • NCBI gene symbol (coding sequence): NP
  • NCBI gene ID (coding sequence): 911830

Analysis of result data

  • How to interpret result?
  • The output page provides a brief description for the virus, a GenBank accession number with a link to the corresponding GenBank web page, brief information regarding the CDS (e.g., gene symbol and gene ID), and detailed information about the top primer pair including the penalty score, forward and backward primer sequences, TaqMan probe, melting temperatures (TM), amplicon size, primer positions, and validation results. Although the MRPrimerV database contains 152,380,247 primer pairs, the output webpage interface does not show all primer pairs in the results, since it might be inconvenient for users. Users can adjust the number of resultant primer pairs for each CDS among Top-1, Top-5, Top-10, and Top-50 by clicking the dropdown menu in the output web page.

    MRPrimerV contains not only primers and probes, but also validation results for some viruses, in particular 12 RNA viruses from the Centers for Disease Control and Prevention (CDC) of Korea. By clicking the “validation results” button, users can view validation data including specimen information, agarose gel data, qPCR amplification and melting curves, and sequencing data of the qPCR amplicon obtained using the selected primer pair.

  • If MRPrimerV cannot find any primers?
  • Not found target gene(s): the set of genes that may be wrong or have typos.