Computational protocol: Filamentous phages prevalent in Pseudoalteromonas spp. confer properties advantageous to host survival in Arctic sea ice

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Protocol publication

[…] RF327 was isolated from BSi20327 and treated with various restriction endonucleases, which showed that it contained restriction sites for HindIII (). Then, the nucleotide sequence of the plasmid was determined by using a combination of subcloning and primer walking. The whole sequence was obtained with at least 3 × coverage. The protein-coding regions were predicted with GeneMarkS for phage at http://topaz.gatech.edu/genemarks.cgi (). Similarity searches were carried out using the BLAST program at http://www.ncbi.nlm.nih.gov/blast (). Signal peptide prediction was implemented using the SignalP 3.0 program at http://www.cbs.dtu.dk/services/SignalP-3.0/ (). The nucleotide sequence of RF327 was submitted to GenBank under the accession number GU198194. The phylogenetic trees based on different filamentous phage proteins were constructed with Molecular Evolutionary Genetics Analysis software (MEGA) () by neighbor joining using the p-distance method. Bootstrap values were calculated based on 1000 computer-generated trees. […]

Pipeline specifications

Software tools GeneMarkS, SignalP, MEGA
Applications Genome annotation, Phylogenetics
Chemicals Hydrogen Peroxide, Sodium Chloride