Computational protocol: A Functional Bacterium-to-Plant DNA Transfer Machinery of Rhizobium etli

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Protocol publication

[…] Protein sequences were compared using the blastp program (PubMed); the percentages of identity of full sequences were calculated as the percentage of identity corrected by the query cover percentage. VirE2 phylogenetic tree was generated using MEGA version 6 [], via the minimum evolution method. The KEGG database release 71.0 (http://www.genome.jp/kegg/) was used to design schematic maps for the different vir regions. […]

Pipeline specifications

Software tools BLASTP, MEGA
Databases KEGG
Application Protein sequence analysis
Organisms Rhizobium etli, Bacteria
Chemicals Nitrogen