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Protocols
- OligoAnalyzer (IDT)
Cool tool for oligo analysis. Features include analysis of hairpin, self-dimer, heter-dimer, and other basic parameters.
http://207.32.43.70/biotools/oligocalc/oligocalc.a...
Added: Wed Mar 24 2004, Hits: 611, Reviews: 0
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- Primer3 (Whitehead Institute/MIT Center for Genome Research)
Very popular primer design tool for designing primers for PCR, hybridization.
http://www-genome.wi.mit.edu/cgi-bin/primer/primer...
Added: Sat Jul 20 2002, Hits: 1560, Reviews: 0
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MethPrimer
(Long-Cheng Li, UCSF)
A free online program for designing primers for methylation specific PCR (MSP) and bisulfite sequencing PCR.
http://itsa.ucsf.edu/~urolab/methprimer/
Added: Thu May 29 2003, Hits: 396, Reviews: 0
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Primerfinder
(Univ. of Texas-SW Med. Ctr)
Easy to use, free, online primer design program
http://eatworms.swmed.edu/~tim/primerfinder/
Added: Sat Jul 20 2002, Hits: 934, Reviews: 0
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Primo
(Chang Bioscience)
Primo online is a friendly PCR primer design tool. It reduces PCR noise by lowering the probability of random primering. Batch mode allows designing for multiple sequences. Users can also calculate the melting temperature using the nearest neighbor model.
http://www.changbioscience.com/primo/primo.html
Added: Tue Oct 08 2002, Hits: 542, Reviews: 0
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The PCR Suite
(Van Baren MJ, Heutink P, Erasmus Medical Center)
a collection of programs that interact with the Whitehead's Primer3 program. The original Primer3 program designs primersets for one sequence and it allows you to change almost every parameter. The PCR Suite has more stringent settings (to allow more working primersets) and a smaller range of parameters (because you won't change most of them anyway).
The suite consists of four programs:
Overlapping_Primers is for creating multiple overlapping PCR products in one sequence.
Genomic_Primers designs primers around exons in genomic sequence. All you need is a GenBank file containing your gene.
SNP_Primers designs primers around every SNP in a GenBank file.
cDNA_Primers designs primers around open reading frames. Simply upload a GenBank file containing your genes.
http://www.eur.nl/fgg/kgen/primer/index.html
Added: Tue Mar 02 2004, Hits: 328, Reviews: 0
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