How to use MRPrimerW
MRPrimerW is available for free and open website for searching desired primers instantly while varying filtering constraints by users.
MRPrimerW has three distinctive features:
(i) searching top-1 primer pairs for multiple target gene(s) that satisfy the user-defined same stringent and allele-invariant constraints for qPCR at once.
(ii) providing search modes: fast mode and exact mode.
(iii) supporting several ways to search, such as by NCBI gene symbol, NCBI CCDS ID, NCBI gene ID, GenBank Accession number, GenBank aliases, or keyword (gene description).
* See more details in About page.
Currently, MRPrimerW provides primers from human and mouse genes.
User may search primers by NCBI gene symbol(s), GenBank Accession number(s), NCBI CCDS ID(s), NCBI gene ID(s), Aliases, or keywords (gene description). User can find exact search terms from NCBI GenBank.
User may search either a single gene or multiple genes.
Examples (for single target gene, species: human)
|Single filtering||primer length||19~23 bp|
|melting temperature (TM)||60~63℃|
|3’ self-complementarity||< 4-mer|
|contiguous residue||< 6-mer|
|End stability (∆G)||>= -9 kcal/mol|
|Pair filtering||length difference||<= 3-mer|
|TM difference||<= 5℃|
|product size||100~250 bp|
|3’ pair-complementarity||< 4-mer|
The first table shows top primer pairs for specific target genes. The second table shows a set of less target-specific primers for the query genes having no result in the first table. Both tables show the top-1 primer pair sequences, GenBank Accession number with link for the details of gene and information on the primer, such as penalty score (i.e. a lower penalty score indicates a better primer), amplicon size, Tm, and position.
Also by default, the output table is sorted by Gene in ascending order (②). The user can sort the output table in various ways: forward position and reverse position in descending or ascending order (⑩ and ⑪).
No primers due to too strict parameters
the set of genes that may have target-specific primer pairs by relaxing filtering constraints and the guidelines how to adjust the constraints.
Not found target gene(s)
the set of genes that may be wrong or have typos.