The JRC GMO-Matrix is an application that takes advantage of the GMO sequence information found in the Central Core DNA Sequence Information System (CCSIS), which are received from companies as part of their legal obligations or extracted from nucleotide / patent sequences databases, as well as the primers and probes sequences of the existing detection methods compiled in the GMOMETHODS database to perform in silico simulations of PCR amplification and, when applicable, probe binding using bioinformatics tools, such as re-PCR and matcher.
JRC GMO-Matrix application relies on a relational database that contains pre-computed values corresponding to the extent of matching between the methods primers and probe and each GMO sequence. Those pre-calculated values represent the results of in silico simulations of the detection of each GMO by each PCR-based detection method and form the core data used by the application for its different case uses. The pre-calculations are made using "re-PCR" (Rotmistrovsky et al, 2004) for detecting potential amplicons and "matcher" from the EMBOSS package (Rice et al. 2000) to test probe annealing when the method contains one
The current version of the JRC GMO-Matrix application contains a set interfaces available to the user, which is expected to grow based on the feedback that will be received.
This interface can be used for building two-dimensional matrices (chosen GMO events vs chosen GMO methods) in order to visualise the universal coverage of the detection methods and identify potential gaps.
This interface allows identification of potential GMO(s) present in the sample based on a set of positive and negative detection method experimental results
The Molecular Biology and Genomics (MBG) Unit of the JRC Institute for Health and Consumer Protection has developed a ready-to-use, multi-target screening tool known as the pre-spotted plate (PSP). This PSP allows testing for the presence of multiple GMO-targets in a single PCR experiment and is therefore expected to offer important advantages in terms of cost and time. This interface provides a web-based tool to facilitate the interpretation of results.
For more information, see:
"JRC GMO-Matrix: a web application to support Genetically Modified Organisms detection strategies."
BMC Bioinformatics. 2014 Dec 30;15(1):6592. link
© European Union, 2014
The information above is provided "as is" without warranty of any kind, either express or implied, including, but not limited to, fitness for a particular purpose and absence of errors in the application. The entire risk as to the use, quality, and performance of the application is with the user. The EU will not be liable for any incidental, consequential, direct or indirect damages including but not limited to the loss of data, loss of profits, or any other financial loss arising from the use or inability to use the application.