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Nucleic Acids Res. 2018 Jan 4;46(D1):D700-D707. doi: 10.1093/nar/gkx1124.

MVP: a microbe-phage interaction database.

Author information

1
Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China.
2
Institute for Computer Science and Cluster of Excellence on Plant Sciences CEPLAS, Heinrich Heine University, 40225 Düsseldorf, Germany.
3
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), No.7 Beitucheng West Road, Chaoyang District, 100029 Beijing, PR China.
4
University of Chinese Academy of Sciences, Beijing 100049, China.
5
Institute of Science and Technology for Brain-Inspired Intelligence (ISTBI), Fudan University, Office 2304, East Main Building of Guanghua Towers, 220 Handan Road, Shanghai 200433, China.
6
European molecular biology laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
7
Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany.
8
Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany.
9
Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.

Abstract

Phages invade microbes, accomplish host lysis and are of vital importance in shaping the community structure of environmental microbiota. More importantly, most phages have very specific hosts; they are thus ideal tools to manipulate environmental microbiota at species-resolution. The main purpose of MVP (Microbe Versus Phage) is to provide a comprehensive catalog of phage-microbe interactions and assist users to select phage(s) that can target (and potentially to manipulate) specific microbes of interest. We first collected 50 782 viral sequences from various sources and clustered them into 33 097 unique viral clusters based on sequence similarity. We then identified 26 572 interactions between 18 608 viral clusters and 9245 prokaryotes (i.e. bacteria and archaea); we established these interactions based on 30 321 evidence entries that we collected from published datasets, public databases and re-analysis of genomic and metagenomic sequences. Based on these interactions, we calculated the host range for each of the phage clusters and accordingly grouped them into subgroups such as 'species-', 'genus-' and 'family-' specific phage clusters. MVP is equipped with a modern, responsive and intuitive interface, and is freely available at: http://mvp.medgenius.info.

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