Phage Genome Annotation Using the RAST Pipeline
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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.
Key wordsPhage Genome annotation RAST Functional annotation Gene predictions
This work was supported by grants from the National Science Foundation MCB-1330800 and DUE-1323809 to RAE. BED was supported by the Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004.
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