PCR Primer Design Tools
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PCR Primer Design Tools
Online PCR primer design tools
Primer 3
The famouse primer design program designed by Steve Rozen and Whitehead Institute for Biomedical Research.
CODEHOP
Introduction: The CODEHOP program designs PCR (Polymerase Chain Reaction) primers from protein multiple-sequence alignments. The program is intended for cases where the protein sequences are distant from each other and degenerate primers are needed.
Gene Fisher
Introduction: This online PCR primer design program processes aligned or unaligned amino acid or nucleotide sequences. It can also be used for degenerate primer design.
Doprimer
Introduction: Doprimer primer design tool can be used for applications targeted on whole genomes or parts of genomes.
Web Primer
This program can design PCR and DNA sequencing primer.
PCR Designer for Restriction Analysis of Sequence Mutations
This primer design tool is for restriction analysis of polymorphisms (SNPs).
Reference:
Bioinformatic tools and guideline for PCR primer design (PDF file) (By Kamel A. Abd-Elsalam)
Last update 08-Feb-2007, Rating Excellent! of 2 votes.
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Write your comment
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1. Length of primer should be 17-28 bases.
2. 50-60% GC content.
3. 3' end with G/C
4. Tm 55-65c
5. No 3' basepairing (complementary).
6. No hairpins.
7. No more than three G/C at 3'.
Rating: Excellent!
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