Computational protocol: Characterization and Genomic Study of Phage vB_EcoS-B2 Infecting Multidrug-Resistant Escherichia coli

Similar protocols

Protocol publication

[…] Putative open reading frames (ORFs) were predicted using artemis software (http://www.sanger.ac.uk/science/tools/artemis) and Glimmer 3 (Aggarwal and Ramaswamy, ), with a threshold of 30 amino acids (aa) as a minimum for the length of protein. Function annotation was performed using the BLAST tools at NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi) against the non-redundant protein sequences database. Transfer RNAs (tRNAs) were identified using tRNAscan-SE (v1.23, http://lowelab.ucsc.edu/tRNAscan-SE) and ribosome RNAs (rRNAs) were determined using RNAmmer (v1.2, http://www.cbs.dtu.dk/services/RNAmmer/). DNAman was used to calculate molecular masses and isoelectric points for predicted phage proteins. The whole viral nucleotide sequence similarities between phages were determined by megablast analysis at NCBI. The global alignment of putative amino acid sequences was carried out by EMBOSS Needle tool at EMBL-EBI (European Molecular Biology Laboratory-European Bioinformatics Institute). Comparison of ORFs from relative phages was performed using EasyFig (http://mjsull.github.io/Easyfig/files.html) (Sullivan et al., ). Phylogenetic analyses between the genomes of related phages were performed with MEGA using the Neighbor-Joining algorithm. […]

Pipeline specifications

Software tools Artemis, Glimmer, tRNAscan-SE, RNAmmer, DNAMAN, BLASTN, EMBOSS, Easyfig
Applications Genome annotation, Phylogenetics, Genome data visualization
Organisms Filamentous phage, Escherichia coli, Shigella phage EP23, Escherichia coli str. K-12 substr. MG1655