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.
JRC GMO-Matrix compiles in silico PCR predictions for GMOs detection.
This function helps control laboratories in designing screening strategies and interpreting the results.
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.
Please select one of these interfaces:
Related publications:
Angers-Loustau, A., et al. "JRC GMO-Matrix: a Web Application to Support Genetically Modified Organisms Detection Strategies." BMC Bioinformatics, 15, no. 417, 2014.