Phage Genome Annotation Using the RAST Pipeline

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

doi:10.1007/978-1-4939-7343-9_17

Phage Genome Annotation Using the RAST Pipeline

Methods Mol Biol. 2018:1681:231-238. doi: 10.1007/978-1-4939-7343-9_17.

Authors

Katelyn McNair¹, Ramy Karam Aziz^{2

3}, Gordon D Pusch³, Ross Overbeek³, Bas E Dutilh^{4

5}, Robert Edwards^{6

7}

Affiliations

¹ Computational Sciences Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.
² Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
³ Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL, 60439, USA.
⁴ Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584, Utrecht, The Netherlands.
⁵ Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525, Nijmegen, The Netherlands.
⁶ Computational Sciences Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA. redwards@mail.sdsu.edu.
⁷ Departments of Biology and Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA. redwards@mail.sdsu.edu.

PMID: 29134599
DOI: 10.1007/978-1-4939-7343-9_17

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: Functional annotation; Gene predictions; Genome annotation; Phage; RAST.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Bacteriophages / genetics*
Base Sequence
Computational Biology / methods*
Genome, Viral*
Molecular Sequence Annotation / methods*