Computational protocol: Production of a single cyclic type of fructooligosaccharide structure by inulin‐degrading Paenibacillus sp. LX16 newly isolated from Jerusalem artichoke root

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Protocol publication

[…] The closest known relatives of the isolate LX16 were identified by performing sequence searches of the GenBank/EMBL database using BLAST (Johnson et al., ) and by utilizing the Ribosomal Database Project‐II (Cole et al., ). The 16S rDNA sequences of the closest relatives were retrieved from the database, aligned using CLUSTALX (Thompson et al., ) and corrected manually. Only unambiguously aligned positions were used for phylogenetic analysis. Distance matrices were produced with the dnadist program of the phylip package software (Felsenstein, ), and an unrooted phylogenetic tree was constructed using the neighbor program contained in the phylip software package (V3.6) (Felsenstein, ). The statistical significance of the obtained groups was assessed by bootstrapping (100 replicates) using the programs seqboot, dnadist, neighbor and consense in the phylip software package. The percentage similarities between the 16S rDNA sequence of strain LX16 and other closely related bacteria were calculated using the MegAlign program in the dnastar software package (DNASTAR, Madison, WI, USA). […]

Pipeline specifications

Software tools Clustal W, PHYLIP
Application Phylogenetics
Organisms Helianthus tuberosus
Chemicals Fatty Acids