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Prophage Hunter: an integrative hunting tool for active prophages.

Publication ,  Journal Article
Song, W; Sun, H-X; Zhang, C; Cheng, L; Peng, Y; Deng, Z; Wang, D; Wang, Y; Hu, M; Liu, W; Yang, H; Shen, Y; Li, J; You, L; Xiao, M
Published in: Nucleic acids research
July 2019

Identifying active prophages is critical for studying coevolution of phage and bacteria, investigating phage physiology and biochemistry, and engineering designer phages for diverse applications. We present Prophage Hunter, a tool aimed at hunting for active prophages from whole genome assembly of bacteria. Combining sequence similarity-based matching and genetic features-based machine learning classification, we developed a novel scoring system that exhibits higher accuracy than current tools in predicting active prophages on the validation datasets. The option of skipping similarity matching is also available so that there's higher chance for novel phages to be discovered. Prophage Hunter provides a one-stop web service to extract prophage genomes from bacterial genomes, evaluate the activity of the prophages, identify phylogenetically related phages, and annotate the function of phage proteins. Prophage Hunter is freely available at https://pro-hunter.bgi.com/.

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Published In

Nucleic acids research

DOI

EISSN

1362-4962

ISSN

0305-1048

Publication Date

July 2019

Volume

47

Issue

W1

Start / End Page

W74 / W80

Related Subject Headings

  • Software
  • Prophages
  • Phylogeny
  • Internet
  • Genome, Bacterial
  • Developmental Biology
  • Bacteriophages
  • 41 Environmental sciences
  • 34 Chemical sciences
  • 31 Biological sciences
 

Citation

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ICMJE
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Song, W., Sun, H.-X., Zhang, C., Cheng, L., Peng, Y., Deng, Z., … Xiao, M. (2019). Prophage Hunter: an integrative hunting tool for active prophages. Nucleic Acids Research, 47(W1), W74–W80. https://doi.org/10.1093/nar/gkz380
Song, Wenchen, Hai-Xi Sun, Carolyn Zhang, Li Cheng, Ye Peng, Ziqing Deng, Dan Wang, et al. “Prophage Hunter: an integrative hunting tool for active prophages.Nucleic Acids Research 47, no. W1 (July 2019): W74–80. https://doi.org/10.1093/nar/gkz380.
Song W, Sun H-X, Zhang C, Cheng L, Peng Y, Deng Z, et al. Prophage Hunter: an integrative hunting tool for active prophages. Nucleic acids research. 2019 Jul;47(W1):W74–80.
Song, Wenchen, et al. “Prophage Hunter: an integrative hunting tool for active prophages.Nucleic Acids Research, vol. 47, no. W1, July 2019, pp. W74–80. Epmc, doi:10.1093/nar/gkz380.
Song W, Sun H-X, Zhang C, Cheng L, Peng Y, Deng Z, Wang D, Wang Y, Hu M, Liu W, Yang H, Shen Y, Li J, You L, Xiao M. Prophage Hunter: an integrative hunting tool for active prophages. Nucleic acids research. 2019 Jul;47(W1):W74–W80.
Journal cover image

Published In

Nucleic acids research

DOI

EISSN

1362-4962

ISSN

0305-1048

Publication Date

July 2019

Volume

47

Issue

W1

Start / End Page

W74 / W80

Related Subject Headings

  • Software
  • Prophages
  • Phylogeny
  • Internet
  • Genome, Bacterial
  • Developmental Biology
  • Bacteriophages
  • 41 Environmental sciences
  • 34 Chemical sciences
  • 31 Biological sciences