PrimerScore2

About us

Description:

This website is free and open to all users, and there is no login requirement.

PrimerScore is a robust high-throughput primer design tool that designs multiple types of primers in one click, including face-to-face, back-to-back, and nested primers, as well as evenly full-covered primers on target regions. PrimerScore precisely evaluates candidate oligos′features, containing specificity, SNPs, dimers, and other basic features. Then it scores the oligos and pairs according to the features using growth curve piecewise function and weighted sum model. Finally, it provides the highest-scoring primer pairs or probes and examines for cross-products and cross-dimers among the outputted primers.

If you encounter any problems, please feel free to contact huaping.zeng@genetalks.com.

Thank you!

Your data is now being processed.You can check the status of your submission at:
Results Link

File:

Enter template sequence (example) or regions (example) or target spots (example)(<=20) to design oligos,
Or Enter pre-designed oligos (example) to be evaluated:
minimum of 2 sequences in FASTA format
Two columns of IDs and Sequences, primer ID must be: xxx-F, xxx-R, xxx-1, xxx-2, probe ID must be xxx-P.
It will take about 20 minutes to extract the information of SNP from dbSNP database.
Template sequences come from database.
or Upload File
Support the above four file types, and note: template sequence filename must be xxx.fa or xxx.fasta.
Database
Database file to check specificity
Common Primer Type
Selecting a common type will automatically set parameters. Keep in mind that "Generic Primer" and "Full-covered Primer" don't support target spots, and "Genotyping Primer" and "Arms Primer" don't support template sequences or regions.
Plex Type
Check cross products and cross dimers among final primers
Check common SNP covered by selected primer sequence and modify to degenerated base

Primer Parameters:

Primer Type
Cover Type
Interval between primers
Interval float ratio
# of pairs to return
Coverage type: "Single" denotes the design aims to design one pair of primers for each template and 3 pairs(set by "# of pairs to return") will be returned; "Full-covered" denotes the design aims to design sevaral pairs of primers evenly distributed across the whole template.
Average Interval between adjacent primers
Floating proportion of interval
Number of primer pairs to return for each target
Primer Melting Temperature
opt
Primer Length
min
max
scale
Step size of primer length from min to max
Distance To SNP
opt_min
opt_max
Min
Max
Distance from Primer 3'end to target spot
Primers Distance
opt_min
opt_max
Min
Max
Distance between two primer 5'ends of a pair, that is product size when primers are face-to-face.

Probe parameters:

Probe Melting Temperature
opt
Probe Length
min
max
Step size of primer length from min to max

Show Advance Parameters:

Check homologous sequence of template sequence.
Not filter any unqualified candidate primers which will consume more running time
Prefix Of Output File
Regions
Enter the position ranges if you want the primers to be located on the designated regions, format is "start,end,scale,fr,start2,end2,scale2,fr2...", fr:F/R/FR, eg.1000,1500,2,F,1200,2000,5,R. It can be given only when inputfile is template file,if not given, will caculate automatically.
Candidate oligos position num
Position number of candidate oligos for a target.
Min Bound Tm
Minimum tm bound to nonspecific region which will creat amplified products.
Max PCR Size
Maximum PCR product size, used when caculate nonspecific products.
Max Products Number
Maximum products number to be caculated, aiming to reduce running time.
Min Efficiency
Minimum amplified efficiency to be passed.
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