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Automated design of mutagenic primers for site-directed mutagenesis


Primer Design:

Primer Characterization






Bioinformatics.Org, which hosts PrimerX, is an international organization which promotes freedom and openness in the field of bioinformatics. This is done by providing free and open resources for research, development and education so that such resources can be further developed. Bioinformatics.Org hopes to lower the barrier to entering and participating in the field of bioinformatics, as access to cutting-edge resources can be prohibitively expensive for those working individually, in small groups, at poorly-funded institutions or in developing nations.

The Primer Generator

The Primer Generator is an automated generator of primers for site-directed mutagenesis. The program analyzes the original nucleotide sequence and desired amino acid sequence and designs a primer that either has a new restriction enzyme site or is missing an old one. This allows for faster sorting out of mutated and non-mutated sequences. If you are designing primers for site-directed mutagenesis, then I highly recommend that you visit this site as well.


NetPrimer is an excellent and user-friendly web-based program for oligonucleotide analysis that utilizes the latest primer design algorithms. While the program is designed for standard PCR primers and is not particularly well-suited for primers used in site-directed mutagenesis, it still has useful features that PrimerX lacks. Particularly, it analyzes primers for the likelihood of secondary structures, such as hairpins, self-dimers, and cross-dimers, which can reduce the efficiency of a PCR reaction. Anybody designing PCR primers of any kind would be served well by this site.

Codon Usage Analyzer

The Codon Usage Analyzer, which I also wrote, is a simple web-based program written to process information from the Codon Usage Database and display it in an easy-to-read format. The program ranks the different codons that can encode each amino acid in order of decreasing frequency, so it becomes easy to determine which codon an organism most frequently uses to encode a particular amino acid. This can be very helpful if you are performing site-directed mutagenesis and you need to select a codon to encode a specific amino acid in a novel mutation.


Bioinformatics.Net is a sponsor-supported catalog of online biological sciences information, specializing in bioinformatics tools. It serves the needs of molecular biologists and other professionals involved in scientific research, including biotechnology and medicine. Its database of BioScience-related tools and free software, which is already very extensive, is continually and rapidly updated with contributions from people around the world.

The Bio-Web

The Bio-Web is a free source for Molecular and Cell Biology-Bioinformatics-Technology news and online bio-resources. It brings daily updated news from major news sources, and all users are welcome to submit articles, interesting links, and topics of discussion for the forums. Anybody interested in up-to-date news on a wide range of biotechnology topics would do well to visit this site.

The objective of the project is to provide a free and exclusive web guide of Polymerase Chain Reaction techniques, with the purpose of facilitating the task search of students, teachers and researchers, and providing a venue for exchanging information among its visitors. If you are looking for information regarding any of the many variants of PCR, then you would do well to visit this site.


StatCounter is a completely free, reliable, invisible, and very excellent web tracking service, providing a highly configurable hit counter as well as real-time detailed stats for monitoring all visitors to a website. While StatCounter has nothing to do with the biological sciences, their service helps me to make PrimerX more useful and available to the public, and I highly recommend this free service to any budding web developer.


BioBanner is a free banner exchange advertising service for the promotion of non-commercial Life Sciences web sites. If you have a web site which meets BioBanner's criteria, you can advertise by exchanging banners with other members. As they have similar sites, and visitors with similar interests, your advertising will be well-targeted.

BioBanner - free advertising for BioScience web sites. BioBanner - free advertising for BioScience web sites.

Last updated: November 27, 2005
Copyright © 2004 by Carlo Lapid