Designing primers with excellent cross-species specificity using MP-Ref (demo link).

1. Select the target database;
2. Enter the targets in BED format;
3. Also select “dog” and “E. coli” as backgrounds databases;
4. And set “Min=0 …

What’s “Long Target Regions”#

If next-generation sequencing (NGS) or short-read sequencing (e.g., PE150) is used to validate amplicons, target regions ​longer than 200 bp​ should be considered ​long target regions (LTRs)​. This is because …

Primer Design for SMN1 Whole Region#

The whole genome sequence of SMN1 has a near identical repeat sequences is from SMN2. Primers for SMN1 also can amplify sequences from SMN2 and can’t be avoidable. So for NGS validation, mutations from amplicons …

This is an example for desinging primers with different amplicon sizes for gel electrophoresis (demo link).

1. Select the target database;
2. Enter the targets in BED format;
3. Choose “Validation method” = “[Multiplex] Size discrimination, e.g., …

Designing primers capable of amplifying both genome A and genome B simultaneously using MP-Ref (demo link)。

1. Select the target database: this time we design primers for mouse and requires these primers should also have exactly one amplicon in human …

This is an example of designing singleplex primers using MP-Ref (demo link).

1. Select the target database;
2. Enter the targets in BED format;
3. Choose “Validation method” = “[Singleplex] Sanger sequencing”;.
4. Below are the results.

What’s the “STR” mode?#

Short Tandem Repeats (STRs) are regions within the genome consisting of multiple repeating DNA sequences. The STR mode is specifically tailored for designing primers to amplify regions flanking STRs or any target …

Introduction#

We have a list of genes, like:

EGFR
MET
TP53

And we want the genome positions plus 10 bases at each end for each exons, the results should like:

chr7	116672185	116672587	NM_000245_exon_0_10_chr7_116672196_f	0	+
chr7	116699060	116700294 …

Introduction#

We have a list of SNP rs numbers, like:

rs1002315756
rs1003815568
rs1004109382
rs1004635980
rs1008829651

And we want the genome positions for each SNPS, the results should like:

#chrom	chromStart	chromEnd	name	ref	altCount	alts	shiftBases …

Introduction#

MPprimer: a program for reliable multiplex PCR primer design

BACKGROUND: Multiplex PCR, defined as the simultaneous amplification of multiple regions of a DNA template or multiple DNA templates using more than one primer set (comprising a …