Computational protocol: Genome Characteristics of a Novel Phage from Bacillus thuringiensis Showing High Similarity with Phage from Bacillus cereus

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Protocol publication

[…] Genomic DNA sequencing was performed by BGI Co. (Beijing, China) with a shotgun sequencing method and the genome was assembled with phrap version 1.080812. Each base had at least five-fold coverage. Open reading frames (ORFs) were predicted with FGENE SV software (http://linux1.softberry.com/berry.phtml?topic=virus&group=programs&subgroup=gfindv) and by visual inspection. ATG, GTG and TTG were used as possible start codons, and 30 codons were taken as a threshold for the ORFs. The BLAST (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi) was used to search for homologous proteins, and the function of each ORF was compared in the CDD database at NCBI (http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml). To search for putative tRNA-encoding genes, tRNAscan-SE 1.21 (http://selab.janelia.org/tRNAscan-SE/) was used. Promoter sequences in the σ70 family were identified by using Bprom (http://linux1.softberry.com/berry.phtml). Dot plot analysis was performed using Nucleic Acid Dot Plots (http://www.vivo.colostate.edu/molkit/dnadot/index.html) with a window size of 13 and a mismatch limit of 0. […]

Pipeline specifications

Software tools tRNAscan-SE, BPROM
Application Genome annotation
Organisms Bacillus thuringiensis, Bacillus cereus, Bacillus anthracis, Bacteria
Chemicals Amino Acids