Computational protocol: Human oropharynx as natural reservoir of Streptobacillus hongkongensis

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Protocol publication

[…] The sequences obtained from the cloned PCR products were analyzed by pairwise alignment, with the optimal GLOBAL alignment parameters, using BioEdit 7.2.0. The sequences of the PCR products were also compared with sequences of closely related species from the DDBJ/ENA/GenBank databases by multiple sequence alignment using MUSCLE 3.8 and were then end-trimmed. Poorly aligned or divergent regions of the aligned, end-trimmed DNA sequences were removed using Gblocks 0.91b with relaxed parameters, and 653 nucleotide positions were included in the final sequence alignment dataset. Tests for substitution models and phylogenetic tree construction using the maximum likelihood method were performed using MEGA 6.06. […]

Pipeline specifications

Software tools BioEdit, MUSCLE, Gblocks, MEGA
Databases DDBJ
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Homo sapiens
Diseases Arthritis, Infectious
Chemicals Nalidixic Acid, Nucleotides, Sulfamethoxazole, Trimethoprim