Phage Genome Annotation Using the RAST Pipeline
Publication date
2018
Authors
McNair, Katelyn
Aziz, Ramy Karam
Pusch, Gordon D
Overbeek, Ross
Dutilh, Bas E.
Edwards, Robert A
Editors
Clokie, M.R.J.
Kropinski, A.M.
Lavigne, R.
Advisors
Supervisors
Document Type
Part of book
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Abstract
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.
Keywords
Phage, Genome annotation, RAST, Functional annotation, Gene predictions, Coronacrisis-Taverne
Citation
McNair, K, Aziz, R K, Pusch, G D, Overbeek, R, Dutilh, B E & Edwards, R A 2018, Phage Genome Annotation Using the RAST Pipeline. in M R J Clokie, A M Kropinski & R Lavigne (eds), Bacteriophages: Methods and Protocols. vol. 3, Methods in Molecular Biology, vol. 1681, Springer, pp. 231-238. https://doi.org/10.1007/978-1-4939-7343-9_17