SNP PCR primer design

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Primo SNP 3.4: SNP PCR Primer Design Click here for more PCR primer design tools.

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Primo SNP 3.4 --- PCR Primer Design for Single Nucleotide Polymorphism (SNP)

Primo SNP has the following options:

SNP Flanking Primers: Designs pairs of primers that flank the SNP site.

Single Base Primer Extension (SBE): Designs primers that anneal immediately next to the SNP site.

Pyrosequencing: Designs pairs of primers that flank the SNP site and pyrosequencing primer next to the SNP site.

Allele Specific-PCR (AS-PCR): Designs primers that will specifically amplify one of the alleles.

Ligase Chain Reaction (LCR): Designs primers that will anneal and ligate for one of the alleles.

PCR-RFLP: Designs primers that will introduce or destroy a restriction site for one of the alleles.

For other SNP detection and identification technologies (e.g. DGGE and TGGE), please visit Primo Melt.

How to use Primo SNP 3.4 --- PCR Primer Design for Single Nucleotide Polymorphism (SNP)

Input your DNA sequences by copy and paste. Polymorphism is denoted by degenerate nucleotide codes as in the NCBI SNP database. An example is shown below:

GAAAACCTCG TTGGCTCAAA GGAAACTGTA G
M
AAATTCTTTT TTTTTATTTT TGTTTTTTAA CTCAAAGAGT GGAGTTTGCA TTGACCTTGT GATGGCACGC TGCTCTTTTG
TTTTGGTGTA AATCCTCTAG TGGGCACTTT GCAAAAGCAA TTTTAGAGCA AAGGTGGTGG CATGGAGTTG TGTGAGGTTG
CTGAAAAGTA GCAAATGGAA GAAAGGTTAA TGGA

Numbers and blank spaces will be ignored. Click on the "Go" button to start. Numbers and blank spaces will be ignored.

For multiple sequences, please check the "Batch mode" checkbox, and input your sequences in the following formart:


>Seq1 name
GAAAACCTCG TTGGCTCAAA GGAAACTGTA G
M
AAATTCTTTT TTTTTATTTT TGTTTTTTAA CTCAAAGAGT GGAGTTTGCA TTGACCTTGT GATGGCACGC TGCTCTTTTG
TTTTGGTGTA AATCCTCTAG TGGGCACTTT GCAAAAGCAA TTTTAGAGCA AAGGTGGTGG CATGGAGTTG TGTGAGGTTG
CTGAAAAGTA GCAAATGGAA GAAAGGTTAA TGGA

>gnl|dbSNP|rs3894_allelePos=181totallen=241|taxid=9606|snpClass=1|alleles='C/T'|mol=genomic|build=36
TAATCAGTCT CCTCCCAGCA AGTGATATGC AACTGAGATT CCTTATGACA CATCTGAACA CTAGTGGATT TGCTTTGTAG
TAGGAACAAG GTACATTCGC GGGATAAATG TGGCCAAGTT TTATCTGCTG CCAGGGCTTT CAAATAGGTT GACCTGACAA
TGGGTCACCT CTGGGACTGA
Y
AATTAGGAAG AGCTGGTACC TAAAATGAAA GATGCCCTTA AATTTCAGAT TCACAATTTT

>gnl|dbSNP|rs3896_allelePos=73totallen=322|taxid=9606|snpClass=1|alleles='C/T'|mol=genomic|build=36
gggtttatac tgacctgcca atgttaaaag ggacctaaat tcactttggg gaagtggcca gaaaggaaga ag
Y
agaaggagaa gagtgcaaga aacctccagt tgtgggggtt gagcctccag gataagaaag aaagaaatct ccagtagggg
ggattgagcc taacacaaac ctttggtaat agacaaggca agacatttcc aataggggag attgagtgtc acctcaaaac
tattaagatg ggaaataccc caggtaagat agagggtaaa aaaggataaa gctagcagca ataacattcc ccctgaaagt
tcCCAATAA

Warning: If the "Batch mode" checkbox is not checked, multiple sequences will be treated as one sequence.

For more PCR primer design tools, please visit Primo Home.

Thanks for using Primo SNP 3.4! Please let us know your suggestions and comments.

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