How To: Metagenomics … in Sao Paulo

The advent of next-generation sequencing has brought the possibility of sequencing not only a single genome but the genomes of a whole community of microorganisms of a biome. We currently know only a small fraction of the viral diversity. The use of metagenomic data and the identification of emerging viruses represent a major challenge in terms of bioinformatics. First, viruses evolve much faster than prokaryotes and eukaryotes, leading to a higher divergence of the sequences and making their detection by conventional pairwise alignment methods more difficult. Second, the number of viral genomes available on public databases is relatively low, compared to archaea and bacteria, for instance. This aspect also makes viral sequence detection and classification much more challenging.

Prof Arthur Gruber from Sao Paulo, Brazil, together with Manja and Kevin, is organizing the III Course on Theoretical and Practical Approaches to Metagenomics and Viral Discovery to be held in Sao Paulo in October.

In this course, they intend to cover some innovative methods that have been recently developed and that can increase the sensitivity of the detection of evolutionary remote viruses. One of the approaches involves the construction and application of profile HMMs. They will teach conceptual aspects of profile HMM construction, especially for taxonomically specific groups of viruses. Also, they will offer practical sessions where the students will be able to build and apply profile HMMs in metagenomic data for viral detection and discovery. They also intend to cover the fundamentals of different machine learning approaches and present in practical sessions different methods applied to viral detection, classification, virus-host interactions, among other topics.

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