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From trees to clouds : PhageClouds for fast comparison of ∼640,000 phage genomic sequences and host-centric visualization using genomic network graphs
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Rangel-Pineros, Guillermo, Millard, Andrew D., Michniewski, Slawomir, Scanlan, David J. , Sirén, Kimmo, Reyes, Alejandro, Petersen, Bent, Clokie, Martha R. J. and Sicheritz-Pontén, Thomas (2021) From trees to clouds : PhageClouds for fast comparison of ∼640,000 phage genomic sequences and host-centric visualization using genomic network graphs. PHAGE : Therapy, Applications, and Research, 2 (4). pp. 194-203. doi:10.1089/phage.2021.0008 ISSN 2641-6530.
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WRAP-From-trees-to-clouds-PhageClouds-for-fast-comparison∼640,000-phage-genomic-sequences-host-centric-visualization-using-genomic-network-graph-2022.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons: Attribution-Noncommercial 4.0. Download (845Kb) | Preview |
Official URL: https://doi.org/10.1089/phage.2021.0008
Abstract
Background: Fast and computationally efficient strategies are required to explore genomic relationships within an increasingly large and diverse phage sequence space. Here, we present PhageClouds, a novel approach using a graph database of phage genomic sequences and their intergenomic distances to explore the phage genomic sequence space.
Methods: A total of 640,000 phage genomic sequences were retrieved from a variety of databases and public virome assemblies. Intergenomic distances were calculated with dashing, an alignment-free method suitable for handling massive data sets. These data were used to build a Neo4j® graph database.
Results: PhageClouds supported the search of related phages among all complete phage genomes from GenBank for a single query phage in just 10 s. Moreover, PhageClouds expanded the number of closely related phage sequences detected for both finished and draft phage genomes, in comparison with searches exclusively targeting phage entries from GenBank.
Conclusions: PhageClouds is a novel resource that will facilitate the analysis of phage genomic sequences and the characterization of assembled phage genomes.
| Item Type: | Journal Article | |||||||||
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| Subjects: | Q Science > QH Natural history Q Science > QR Microbiology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | |||||||||
| SWORD Depositor: | Library Publications Router | |||||||||
| Library of Congress Subject Headings (LCSH): | Bacteriophages -- Genetics, Genomics, Computational biology | |||||||||
| Journal or Publication Title: | PHAGE : Therapy, Applications, and Research | |||||||||
| Publisher: | Mary Ann Liebert | |||||||||
| ISSN: | 2641-6530 | |||||||||
| Official Date: | 16 December 2021 | |||||||||
| Dates: |
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| Volume: | 2 | |||||||||
| Number: | 4 | |||||||||
| Page Range: | pp. 194-203 | |||||||||
| DOI: | 10.1089/phage.2021.0008 | |||||||||
| Status: | Peer Reviewed | |||||||||
| Publication Status: | Published | |||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||
| Date of first compliant deposit: | 8 July 2022 | |||||||||
| Date of first compliant Open Access: | 8 July 2022 | |||||||||
| RIOXX Funder/Project Grant: |
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