Viruses play an important role in marine ecology, but their diversity and exact roles remain unclear. It seems particularly interesting to make use of the newly available metagenomics data collected from the TARA-Oceans program, to start evaluating the diversity and the impact of marine viruses. Nonetheless, viruses harbor a high mutation rate in their genome, which makes difficult their correct identification. The aim of this internship was to improve viruses identification in metagenomics data exploring two different type of information for characterizing two viral proteins families : the RNA-dependent RNA-polymerases (RdRps), which is conserved in primary sequence and is found in all RNA viruses, and the capsid proteins, which are characteristic of viruses, and are conserved in structure. The characterization of RdRps sequences has confirmed the difficulty to identify them because of the high mutation rate, and the difficulty to discriminate them from eukaryotics RdRps. This was the case for all the different methods we applied, like BLAST, HMMER and Protomata, and even with the parameter optimization done for this last one. The study of the specificity of contact fragments (pair of carbon ribbons segments interacting ) of capsid proteins was very promising. Indeed, it allowed us to identify characteristic fragments of viruses.