Computational protocol: Evidence for Conserved Function of γ–Glutamyltranspeptidase in Helicobacter Genus

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Protocol publication

[…] Phylogenetic analyses of γGT amino acid sequences were conducted in MEGA4 using the Minimum Evolution (ME) method. The amino acid sequences were aligned using MAFFT . The evolutionary distances were computed using the Dayhoff matrix-based method, and the ME tree was searched using the Close-Neighbor-Interchange (CNI) algorithm (level 1). All positions containing alignment gaps and missing data were eliminated in pairwise sequence comparisons . A multi-alignment of ggt sequences of Helicobacter spp and C. jejuni was built in MEGA4 on the basis of the amino acid sequence alignment. Maximum likelihood (ML) trees were constructed using PHYML with a nucleotide evolution model selected by FindModel (http://www.hiv.lanl.gov/). Trees were visualized by iTOL . Non-synonymous/synonymous substitution (Ka∶Ks) was evaluated by sliding window analysis (window size of 50 bp) using SWAKK . […]

Pipeline specifications

Software tools MEGA, MAFFT, PhyML, iTOL, SWAKK
Applications Phylogenetics, Protein sequence analysis
Organisms Helicobacter pylori, Mus musculus, Homo sapiens
Diseases Infection