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Identifying distant homologous viral sequences in metagenomes using protein structure information

Name: Identifying distant homologous viral sequences in metagenomes using protein structure information
Keywords: [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.EE.BIO] Life Sciences [q-bio]/Ecology, environment/Bioclimatology, remote homology, virus, metagenomic

appsOther research productkeyboard_double_arrow_right Other ORP type English Funded by:TARA | Tara Oceans

Authors: Boccara, Martine; Carpentier, Mathilde; Chomilier, Jacques; Coste, François; Galiez, Clovis; Pothier, Joël; Veluchamy, Alaguraj;

Identifying distant homologous viral sequences in metagenomes using protein structure information

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Abstract

It is estimated that marine viruses daily kill about 20% of the ocean biomass. Identifying them in water samples is thus a biological issue of great importance. The metagenomic approach for virus identication is a challenging task since their sequences carry a lot of mutations making them hardly possible to find by standard homology searches. The PEPS VAG project aims at establishing a novel methodology that uses structures of proteins as extra-information in order to annotate metagenomes without relying on homology of sequences. In the context of the first experiments made on the metagenome of station 23 of the TARA Ocean Project, we use the structures of capsid protein to infer the sequence signature of their fold, in order to find them in the metagenome. We present here the methodology, the first experiments and the on-going improvements.

Keywords

[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.EE.BIO] Life Sciences [q-bio]/Ecology, environment/Bioclimatology, remote homology, virus, metagenomic

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European Marine Science