Tandemizer

About Tandemizer

Tandem repeat sequences occur in abundance throughout the genomes of prokaryotic organisms and individual tandem repeat arrays can be used as genetic or phylogenetic markers. During an initial examination of tandem arrays between pairs of bacterial genomes it was observed that tandem array blocks (TABs - multiple, ordered tandem repeat array loci separated by identical or similar spacer regions) appeared to be shared, with numbers of shared blocks correlating with degree of relatedness.

We therefore designed a Java tool, Tandemizer, which uses output from the MUMmer suite "exact-tandems" program, combined with whole-genome sequences and optional GenBank files, to graphically compare TABs among two or more prokaryotic whole genomes. Tandemizer is an extensible, flexible tool that allows visualization of whole-genome arrangement among many genomes based upon TABs, with correlations to GenBank annotations for genes and other features, and drill-down to the sequence level for polymorphism analysis. Tandemizer has been used to visually assess degree of relatedness among the genomes of Francisella, Staphylococcus, and Streptococcus, to search for correlations with markers for virulence and antibiotic resistance, and to assess relationship of IS elements to rearrangements among genomes.

Several enhancements are underway or planned, including allowance for degenerative tandem repeat array loci, correlation with known SNP loci discovered using SIDACS (a SNP and Indel Discovery And Classification System based on MUMmer and developed jointly between TGen and NAU), saving SNP loci for marker assay development, and inclusion of unfinished genomes containing multiple contigs.

Copyright and Licensing

Tandemizer is copyright 2007 by The Translational Genomics Research Institute. All rights reserved. This License is limited to, and you may use the Software solely for, your own internal and non-commercial use for academic and research purposes. Without limiting the foregoing, you may not use the Software as part of, or in any way in connection with the production, marketing, sale or support of any commercial product or service. For commercial use, please contact licensing@tgen.org. By installing this Software you are agreeing to the terms of the LICENSE file distributed with this software.

In any work or product derived from the use of this Software, proper attribution of the authors as the source of the software or data must be made.