In silico PCR simulation
Against complete bacterial and archaeal genomes
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Information about the service

The ability to rapidly and accurately simulate PCR experiments is a valuable tool for both educational and research purposes. With the development of our PCR simulation service against complete bacterial and archaeal genomes, we aim to provide a valuable resource for researchers and students alike. The service is freely available, and allows users to view the amplicon types obtained from each sequence searched. This information can be used to help design PCR experiments, and assess the potential success of a specific PCR primer pair.

The list of genomes and their sequences are regularly updated from NCBI-Assembly. Only complete genome sequences are downloaded. Last update: 2023/06/06.

  • Complete archaeal genomes: 577
  • Complete bacterial genomes: 39198

This site has been developed by Dr. Joseba Bikandi and co-workers in the Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, in the University of the Basque Country.

How to simulate a PCR experiment:

  • Enter a search term (for example a genera - Bacillus -) to select among the genomes included in the database. The system distinguishes uppercase and lowercase.
  • Enter the primers. The current version of the program only works for primers longer than 15 bp. Primers must not contain degenerate nucleotides and they must be writen in the 5'-3' direction.


  • The in silico experiment allows 3 mismatches between the primers and the target DNA.
  • The maximum length of amplicons computed is 2000 bp.
  • Extrachromosomal DNA is included in the simulation when available.
  • Althought computing requires less than a second to perform a PCR simulation per genome (up to 7 experiments may be computed per second), in case the search term (p.e.: a genera) recruits many genomes, the total computing may be very long.
  • The service provides a link to the PCR experiment. Save it for your records. The experiment will be stored in our server for 1 month prior to automatic deletion.

We are open to suggestions

Citing this site

If information obtained from this site is used in scientific publications, please cite the following paper:
Bikandi, J., San Millan, R., Rementeria, A., and Garaizar, J. 2004. In silico analysis of complete bacterial genomes: PCR, AFLP-PCR, and endonuclease restriction. Bioinformatics 20:798-9.
DOI: 10.1093/bioinformatics/btg491

Privacy policy

The service is freely available, and no data is recorded from users but for usage statistics.


This software is an aid for your work. However, we do not claim that the analysis performed by these software is exhaustive. can not take any responsibility for consequences that might occur through their use.