Computational protocol: A marine inducible prophage vB_CibM-P1 isolated from the aerobic anoxygenic phototrophic bacterium Citromicrobium bathyomarinum JL354

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Protocol publication

[…] The draft genome sequence of C. bathyomarinum JL354 is available under the GenBank accession number NZ_ADAE00000000. The JL354 genome was manually analyzed for the presence of a putative prophage. First, the genome was scanned for phage-related genes. When a phage-related gene cluster (ZP_06862281-ZP_06862290) was encountered, the surrounding genes were also examined. Putative prophage fragments were re-annotated by performing a PSI-BLAST search against the GenBank database for further analysis. The beginning and end of a specific prophage genome were estimated based on the annotations of surrounding genes. The complete prophage genome was used to predict lifestyle with the Phage Classification Tool Set (PHACTS) (http://www.phantome.org/PHACTS/).A tRNA search was performed in the prophage genome using tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE). Homologous prophages from Hoeflea phototrophica DFL-43 (NZ_ABIA00000000) and bacteriophage Mu (NC_000929) were used for comparative genomic analysis with the prophage found in C. bathyomarinum JL354.Nearly complete major head (>900 bp) gene was used to construct a phylogenetic tree. All sequences collected from the NCBI database were aligned using Clustal X, and phylogenetic trees were constructed using the neighbor-joining and maximum-likelihood algorithms in MEGA software 5.0. The phylogenetic trees were supported by bootstrap for resampling test with 1000 and 100 replicates using neighbor-joining and maximum-likelihood algorithms respectively. […]

Pipeline specifications

Software tools BLASTP, Phage Classification Tool Set, tRNAscan-SE, Clustal W, MEGA
Applications Genome annotation, Phylogenetics
Chemicals Mitomycin