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In Silico Biology 5, 0031 (2005); ©2005, Bioinformation Systems e.V.  

In silico simulation of fingerprinting techniques based on double endonuclease digestion of genomic DNA

Rosario San Millán, Javier Garaizar and Joseba Bikandi*

Department of Immunology, Microbiology and Parasitology, University of the Basque Country, Paseo de la Universidad, 7, 01006 Vitoria-Gasteiz, Spain.

*  Corresponding author; fax +34-945-013014; Email:

Edited by H. Michael; received March 14, 2005; revised and accepted April 06, 2005; published April 11, 2005


We have developed an online generic tool for simulation of fingerprinting techniques based on the double endonuclease digestion of DNA. This tool allows modelling and modifications of already existing techniques, as well as new theoretical approaches not yet tried in the lab. It allows the use of any combination of recognition patterns and discrimination of end types yielded by restriction with non palindromic recognition sizes. Re-creation of experimental conditions in silico saves time and reduces laboratory costs. This tool allows simulation of Amplified Fragment Length Polymorphism (AFLP-PCR), Subtracted Restriction Fingerprinting (SRF), and additional novel fingerprinting techniques. Simulation may be performed against custom sequences uploaded to the server, or against all sequenced bacterial genomes. Different endonuclease types may be selected from a list, or a recognition sequence may be introduced in the form. After double digestion of DNA, four fragment types are yielded, and the program allows their customised selection. Selective nucleotides may be used in the experiment. Scripts for specific simulation of AFLP-PCR and SRF techniques are available, and both include a suggestion tool for the selection of endonucleases. This is the first program available for the simulation of SRF fingerprinting.

Availability: This free online tool is available at

Keywords: restriction digest, double digest, AFLP-PCR, Subtracted Restriction Fingerprinting (SRF), data mining, in silico analysis, genotyping, endonuclease, bacterial genomes