In the gene identification process, MG-RAST employs a machine learning approach known as FragGeneScan. This method is utilized to identify gene sequences within the metagenomic or metatranscriptomic data.
For the identification of ribosomal RNA sequences, MG-RAST initiates a BLAT search against a reduced version of the SILVA database. This step allows the system to pinpoint and categorize ribosomal RNA sequences within the dataset, contributing to a more detailed understanding of the biological composition of the analyzed metagenomes or metatranscriptomes.