Computational protocol: Bacillus marcorestinctum sp. nov., a Novel Soil Acylhomoserine Lactone Quorum-Sensing Signal Quenching Bacterium

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Protocol publication

[…] The closely known relatives of the new LQQ isolate were determined by performing sequence searches in the GenBank/EMBL database using BLAST program [] and at Ribosomal Database Project-II []. The 16S rRNA gene sequences of these closely related strains were retrieved from the databases. These sequences were aligned using CLUSTAL X program [] and corrected manually. Only unambiguously aligned positions were used for phylogenetic analysis. Distance matrices were produced with the DNADIST program of the PHYLIP package [] and a phylogenetic unrooted tree was constructed using the NEIGHBOR program contained in the PHYLIP software package (V3.6) []. The statistical signification of the groups obtained was assessed by bootstrapping (100 replicates) using the program SEQBOOT, DNADIST, NEIGHBOR and CONSENSE []. The percentage similarities of 16S rRNA gene sequence of strain LQQ with other closely relative bacteria were calculated using Megalin program in DNASTAR package (DNASTAR, Inc., Madison, WI, USA). The GenBank accession numbers are shown in and the similarity for strains examined in this paper was given in . […]

Pipeline specifications

Software tools Clustal W, PHYLIP
Application Phylogenetics
Organisms Bacillus anthracis, Brevibacillus brevis
Diseases Dysentery, Bacillary
Chemicals Carbon, Glucose