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| Item Type: | Article |
|---|---|
| Title: | MVP: a microbe-phage interaction database |
| Creators Name: | Gao, N.L., Zhang, C., Zhang, Z., Hu, S., Lercher, M.J., Zhao, X.M., Bork, P., Liu, Z. and Chen, W.H. |
| 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. |
| Keywords: | Archaea, Bacteria, Bacterial DNA, Bacteriophages, Base Sequence, Datasets as Topic, Factual Databases, Gastrointestinal Microbiome, Genetic Databases, Host Specificity, Metagenomics, Nucleic Acid Sequence Homology, Prophages, Species Specificity, Viral DNA, Viral Genome, Virus Integration |
| Source: | Nucleic Acids Research |
| ISSN: | 0305-1048 |
| Publisher: | Oxford University Press |
| Volume: | 46 |
| Number: | D1 |
| Page Range: | D700-D707 |
| Date: | 4 January 2018 |
| Official Publication: | https://doi.org/10.1093/nar/gkx1124 |
| PubMed: | View item in PubMed |
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