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online PCR primer design
Category: PCR primers design
Primer Blast allows: to design PCR primers
Primer Blast is a web application that uses Primer3 to design PCR primers and then submits them to BLAST search against user-selected database. The blast results are then automatically analyzed to avoid primer pairs that can cause amplification of targets other than the input template.
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OligoCalc is a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intra-molecular hairpin loop formation. OligoCalc has a familiar ‘calculator’ look and feel, making it readily understandable and usable. OligoCalc incorporates three common methods for calculating
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Primer3 Plus is the new improved web interface to the popular Primer3 primer design program.
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QuantPrime is very user-friendly tool for primer pair design in small- to large-scale real-time reverse transcription qPCR analyses. It offers design and specificity checking with highly customizable parameters and is ready to use with most publicly available eukaryotic transcriptomes, including all higher eukaryote model organisms and important plant crops, while benefiting from exon-intron border and splice variant information in available genome annotations.
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A very intuitive tool to design primer. The request need the entering of gene sequence or sequence of interest (multiple sequences in FASTA format with exons in uppercase letters and introns in lowercase letters, positive orientation). A complete tutorial is available.
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GeneFisher2 is a very good site allowing great control over primer design
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Upload a file containing Fasta-formatted DNA sequences or alternatively a *.aln file, select the control one wants over the primer design from an extensive list
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Primer3 is a very powerful PCR primer design online application permitting one considerable control over the nature of the primers, including size of product desired, primer size and Tm range, and presence/absence of a 3’-GC clamp.
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This online program helps to evaluate the quantity of primers and nucleotides for optimal PCR reaction and the necessary number of cycles.
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