Phage Genome Annotation Using the RAST Pipeline

Katelyn McNair, Ramy Karam Aziz, Gordon D. Pusch, Ross Overbeek, Bas E. Dutilh, Robert Edwards

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

51 Citations (Scopus)


Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis. We provide a road map through the phage genome annotation pipeline, and discuss the challenges and solutions for phage genome annotation as we have implemented in the rapid annotation using subsystems (RAST) pipeline.

Original languageEnglish
Title of host publicationBacteriophages
Subtitle of host publicationMethods and Protocols, Volume 3
EditorsMartha R. J. Clokie, Andrew M. Kropinski, Rob Lavigne
Place of PublicationNew York, NY
PublisherHumana Press
Number of pages8
ISBN (Electronic)9781493973439
ISBN (Print)9781493973415
Publication statusPublished - 2018
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Functional annotation
  • Gene predictions
  • Genome annotation
  • Phage
  • RAST


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