GMO-Matrix
Assembles two-dimensional matrices (chosen GMO events vs chosen GMO methods) to visualise the analytical coverage of the methods and identify potential gaps in the users screening approach.
Last update: 27/07/2023
JRC GMO-Matrix compiles in silico PCR predictions for GMOs detection.
This function helps control laboratories in designing screening strategies and interpreting the results. Alternatively, JRC GMO-Screen provides proposals for a general screening, for screening EU authorised GMOs or for the interpretation of pre-spotted plates. These functions are based on in silico analysis.
The computer simulations are performed using primers and probe sequences from the GMOMETHODS database and GMOs sequences from the JRC internal database. The latter includes sequences provided by the applicants for authorisation of GMOs or retrieved independently from nucleotide/patent databases. The scripts that simulate PCR amplification use "re-PCR" (Rotmistrovsky et al, 2004) for detecting potential amplicons in GMO sequences and "matcher" from the EMBOSS package (Rice et al. 2000) for verifying probe annealing when the method contains one. The information on the authorisation status of GMOs is automatically extracted on a daily basis from the Community register of GM food and feed.
Please select one of these interfaces:
Related publications:
Bonfini, L., "In Silico Proposal of Screening Strategies for Detecting EU Authorised GMOs." European Commission, Ispra, JRC131782, 2023.
Angers-Loustau, A., et al. "JRC GMO-Matrix: a Web Application to Support Genetically Modified Organisms Detection Strategies." BMC Bioinformatics, 15, no. 417, 2014.
Rosa, S. F., et al. "Development and applicability of a ready-to-use PCR system for GMO screening." Food Chemistry, 15 June 2016, vol. 201, pp. 110-119.
Angers-Loustau, A., et al. "Using the EURL GMFF Online Bioinformatics Resources: A how-to Guide for Practical JRC GMO-Matrix and JRC GMO-Amplicons Case Uses." European Commission, Ispra, JRC101853, 2016.