Computational protocol: Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia

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[…] Genomes were aligned using the MAUVE genome alignment program version 2.1.1 []. Original alignment of the genomes was done with a minimum backbone setting of 100 bp. Local colinear block (LCB) weight of this alignment was increased until only 29 LCB's were identified by the program. LCB order numbers were then input to the GRIMM web server for rearrangement modeling [] to determine which genome had fewer rearrangement events from the node of the trifurcation. Strain ACN was determined to have fewer LCR events and was used as an alignment standard. Subsequent MAUVE alignment of the genomes used a minimum backbone of 1200 bp, with a 500 bp minimum island value to eliminate spurious LCB assignments. Backbone and island files were visualized using the Genvision plugin for Adobe Illustrator©. […]

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