| Chapter title |
Phage Genome Annotation Using the RAST Pipeline
|
|---|---|
| Chapter number | 17 |
| Book title |
Bacteriophages
|
| Published in |
Methods in molecular biology, January 2018
|
| DOI | 10.1007/978-1-4939-7343-9_17 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-7341-5, 978-1-4939-7343-9
|
| Authors |
Katelyn McNair, Ramy Karam Aziz, Gordon D. Pusch, Ross Overbeek, Bas E. Dutilh, Robert Edwards, McNair, Katelyn, Aziz, Ramy Karam, Pusch, Gordon D., Overbeek, Ross, Dutilh, Bas E., Edwards, Robert |
| 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. |
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