Affiliations: Department of Immunology, Microbiology and
Parasitology, University of the Basque Country, Paseo de la Universidad, 7,
01006 Vitoria-Gasteiz, Spain
Abstract: 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.
Keywords: restriction digest, double digest, AFLP-PCR, Subtracted Restriction Fingerprinting (SRF), data mining, in silico analysis, genotyping, endonuclease, bacterial genomes
