A simulation tool for the study of symmetric inversions in bacterial genomes

Authors:
Ulisses Dias;Zanoni Dias;João C. Setubal
Affiliations:
Institute of Computing, Unicamp, Campinas, SP, Brazil and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA;Institute of Computing, Unicamp, Campinas, SP, Brazil;Virginia Bioinformatics Institute and Department of Computer Science, Virginia Tech, Blacksburg, VA
Venue:
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Year:
2010

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Abstract

We present the tool SIB that simulates genomic inversions in bacterial chromosomes. The tool simulates symmetric inversions but allows the appearance of nonsymmetric inversions by simulating small syntenic blocks frequently observed on bacterial genome comparisons. We evaluate SIB by comparing its results to real genome alignments. We develop measures that allow quantitative comparisons between real pairwise alignments (in terms of dotplots) and simulated ones. These measures allow an evaluation of SIB in terms of dendrograms. We evaluate SIB by comparing its results to whole chromosome alignments and maximum likelihood trees for three bacterial groups (the Pseudomonadaceae family and the Xanthomonas and Shewanella genera). We demonstrate an application of SIB by using it to evaluate the ancestral genome reconstruction tool MGR.