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Phage orthologous clusters: a database of phage information

Grant number: 15/14334-3
Support type:Scholarships abroad - Research Internship - Master's degree
Effective date (Start): November 04, 2015
Effective date (End): May 03, 2016
Field of knowledge:Interdisciplinary Subjects
Principal Investigator:João Carlos Setubal
Grantee:Deyvid Emanuel Amgarten
Supervisor abroad: Chris Upton
Home Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Local de pesquisa : University of Victoria (UVic), Canada  
Associated to the scholarship:14/16450-8 - Diversity analysis of bacteriophages associated to microbial community during the composting process, BP.MS


Phages studies have been experiencing a resurgence of scientific interest due to recent evidences that show their importance in microbial ecology, carbon and other nutrients cycling and potential applications as anti-bacterial therapeutics in clinical, agricultural and food processing fields. They are also theorized as Nature reservoirs of genetic diversity, being responsible for new genes and protein products incorporated in prokaryotic and eukaryotic organisms. The composting biomass degradation process has been studied in our group though metagenomic and meta-transcriptomic techniques and millions of sequencing reads were generated. These data are being studied by customized pipelines and methodologies and annotation faces a need for references in viral sequences and orthology information. Professor Upton's group is responsible for the Viral Bioinformatics Resource Center, a reference platform for virologists around the world. His group is also responsible for the Virus Orthologous Clusters (VOCs) database, which catalogues genomic and orthology information about large DNA viruses. In this way, the main goal of this BEPE proposal is to create a database of Phage Orthologous Clusters (PhOCs) having VOCs as a model. The database will be structured with (1) Complete phage genomes and (2) annotations, ORFs, nucleotide and amino acid frequencies, codon use, BLASTP scores, and orthologous cluster membership data for each gene. The new PhOCs database is intended to be a reference database of phage genomic information and orthologous clusters. Implementation includes development of JAVA web start applications and GUI user friendly interface. This work will help to characterize composting assembled contigs and other viral sequences from environmental samples, being public available for scientific community.

Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
AMGARTEN, DEYVID; MARTINS, LAYLA FARAGE; LOMBARDI, KAREN CRISTINA; ANTUNES, LUCIANA PRINCIPAL; SILVA DE SOUZA, ANA PAULA; NICASTRO, GIANLUCCA GONCALVES; KITAJIMA, ELLIOTT WATANABE; QUAGGIO, RONALDO BENTO; UPTON, CHRIS; SETUBAL, JOAO CARLOS; DA SILVA, ALINE MARIA. Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages. BMC Genomics, v. 18, MAY 4 2017. Web of Science Citations: 6.

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