Computational protocol: Decoding the genetic and functional diversity of the DSF quorum sensing system in Stenotrophomonas maltophilia

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Protocol publication

[…] Sequences of the rpf cluster and corresponding genes from selected Xanthomonadales strains were retrieved from their respective NCBI genome sequences [http://www.ncbi.nlm.nih.gov/genome/]. The recently described genome sequence of S. maltophilia M30 (Huedo et al., ) was used as a reference for the rpf-2 variant. To manually confirm some annotations, orthology relations were defined as reciprocal best matches by blastn and blastx. Concatenated nucleotide sequences for the rpfF and rpfC genes were aligned using ClustalW as implemented in MEGA 6 (Tamura et al., ) with default parameters. rpfH was also included in the analysis, if present. Neighbour-joining trees were generated and displayed using MEGA 6. The GARD program (Kosakovsky Pond et al., ) was used to search for putative recombination breakpoints in sequence alignments. Detailed information about the sequences analyzed in recombination tests is found in Supplementary Material (File ). […]

Pipeline specifications

Software tools BLASTN, BLASTX, Clustal W, MEGA
Organisms Stenotrophomonas maltophilia
Chemicals Fatty Acids